SSc Methylation Combined Analysis
SSc Methylation Combined Analysis
- 1 Part 0: 450K microarray data analysis
- 1.1 Confirmation of the purified cell type
- 1.2 PCA of SSc as well as control samples using CD4+ and CD8+ T cells
- 1.3 Differential Methylation Analysis of CD4+ T cells
- 1.4 Differential Methylation Analysis of CD8+ T cells
- 1.5 Differential Methylation Analysis of CD4+ and CD8+ T cells
- 1.6 Gene Ontology Analysis of CD4+ T cells
- 1.7 Gene Ontology Analysis of CD8+ T cells
- 2 Part 1: MethylTarget Technology Evaluation and Quality Control
- 2.1 Quality Control:The average coverage of each sample, each CpGsite, and each gene (average coverage of the CpGsites in a gene)
- 2.2 Correlation of MethylTarget Technology and Methylation 450K technology with same samples and same CpGsites in CD4+/CD8+
- 2.2.1 Table 4: The Correlation of each CpGsite between two techniques in CD4+ and CD8+ T cells
- 2.2.2 Table 5: The Correlation of each CpGsite between two techniques in CD4+ T cells
- 2.2.3 Table 6: The Correlation of each CpGsite between two techniques in CD8+ T cells
- 2.2.4 Figure1: The Correlation of all CpGsites between two techniques in CD4+ T cells
- 2.2.5 Figure2: The Correlation of all CpGsites between two techniques in CD8+ T cells
- 2.2.6 Figure3: The Correlation of all CpGsites between two techniques in CD4+ and CD8+ T cells
- 2.2.7 Figure4 : The correlation between the correlation r^2 and coverage depth
- 2.3 Part I Summary:
- 3 Part II: Validation of differential methylated CpGsites with MethylTarget technology
- 3.1 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD4+
- 3.1.1 Validation of differential methylated CpGsites between SSc patients and Controls
- 3.1.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
- 3.1.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
- 3.1.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
- 3.2 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD8+
- 3.2.1 Validation of differential methylated CpGsites between SSc patients and Controls
- 3.2.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
- 3.2.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
- 3.2.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
- 3.3 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD4+
- 3.3.1 Validation of differential methylated CpGsites between SSc patients and Controls
- 3.3.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
- 3.3.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
- 3.3.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
- 3.4 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD8+
- 3.4.1 Validation of differential methylated CpGsites between SSc patients and Controls
- 3.4.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
- 3.4.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
- 3.4.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
- 3.5 PartII Summary:
- 3.1 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD4+
- 4 Part III: Differential gene expression in CD4+/CD8+ T cells and its correlation with gene methylation
- 4.1 Differential gene expression in CD4+ T cells between SSc patients and Controls
- 4.2 Differential gene expression in CD8+ T cells between SSc patients and Controls
- 4.3 Correlation between gene expression and methylation in CD4+ T cells
- 4.4 Correlation between gene expression and methylation in CD8+ T cells
- 4.5 Correlation between gene expression and methylation in CD4+ and CD8+ T cells
- 4.6 PartIII Summary:
- 5 Part IV: Differential serum type I IFN level and its correlation with gene expression and methylation
- 5.1 Figure 25: Differential serum type I IFN alpha level between SSc patients and Controls
- 5.2 Figure 26: Differential serum type I IFN beta level between SSc patients and Controls
- 5.3 Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells
- 5.4 Correlation of serum type I IFN beta level and gene expression in CD4+ T cells
- 5.5 Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells
- 5.6 Correlation of serum type I IFN beta level and gene expression in CD8+ T cells
- 5.7 Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
- 5.7.1 Table 31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
- 5.7.2 Figure31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
- 5.7.3 Table 32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells
- 5.7.4 Figure32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells
- 5.8 Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells
- 5.9 Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells
- 5.10 PartIV Summary:
- 6 Part V: INF treating for Cell Line
- 7 Part VI: The Methylation Status of the Differentially Methylated CpGsites in other autoimmune diseases
## Warning: package 'knitr' was built under R version 3.2.5
1 Part 0: 450K microarray data analysis
1.1 Confirmation of the purified cell type
1.2 PCA of SSc as well as control samples using CD4+ and CD8+ T cells
1.3 Differential Methylation Analysis of CD4+ T cells
1.3.1 Basic Description of CD4+ T cells
[1] "1.Total probes remained: 400420"
[1] "2.Number of the total DMS: 1026"
[1] "3.Number of the hyper DMS: 740"
[1] "4.Number of the hypo DMS: 286"
[1] "5.Number of the genes of the DMS: 621"
[1] "6.Number of the genes of the hyper DMS: 440"
[1] "7.Number of the genes of the hypo DMS: 175"
[1] "8.Number of the genes of the mixed DMS: 6"
[1] "9.Number of the probes located at the promoter: 257"
[1] "10.Number of the genes of the probes located at the promober: 173"
[1] "11.Number of the genes of the hyper probes located at the promober: 117"
[1] "12.Number of the genes of the hypo probes located at the promober: 56"
[1] "13.Number of the genes of the mixed probes located at the promober: 0"
1.4 Differential Methylation Analysis of CD8+ T cells
1.4.1 Basic Description of CD8+ T cells
[1] "1.Total probes remained: 400491"
[1] "2.Number of the total DMS: 2613"
[1] "3.Number of the hyper DMS: 1830"
[1] "4.Number of the hypo DMS: 783"
[1] "5.Number of the genes of the DMS: 1567"
[1] "6.Number of the genes of the hyper DMS: 1086"
[1] "7.Number of the genes of the hypo DMS: 412"
[1] "8.Number of the genes of the mixed DMS: 69"
[1] "9.Number of the probes located at the promoter: 795"
[1] "10.Number of the genes of the probes located at the promober: 500"
[1] "11.Number of the genes of the hyper probes located at the promober: 332"
[1] "12.Number of the genes of the hypo probes located at the promober: 166"
[1] "13.Number of the genes of the mixed probes located at the promober: 2"
1.5 Differential Methylation Analysis of CD4+ and CD8+ T cells
[1] "1.Number of the shared significant CpGsites : 330"
[1] "2.Number of the unique significant CpGsites of CD4+ : 696"
[1] "3.Number of the unique significant CpGsites of CD8+ : 2283"
[1] "4.Number of the shared significant Genes : 215"
[1] "5.The accordance rate of the shared CpGsites: 1.000000"
[1] "6.The number of the hypermethylation genes of the shared Significant CpGsites : 138"
[1] "7.The number of the hypomethylation genes of the shared Significant CpGsites : 75"
[1] "8.The number of the mixed genes of the shared Significant CpGsites : 2"
1.6 Gene Ontology Analysis of CD4+ T cells
| GOMFID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|
| GO:0034340 | 0.0000054 | 17.650969 | 0.4819461 | 6 | 25 | response to type I interferon |
| GO:0060337 | 0.0000054 | 17.650969 | 0.4819461 | 6 | 25 | type I interferon signaling pathway |
| GO:0048525 | 0.0001584 | 11.926537 | 0.5397797 | 5 | 28 | negative regulation of viral process |
| GO:0045071 | 0.0003135 | 15.452784 | 0.3470012 | 4 | 18 | negative regulation of viral genome replication |
| GO:0042168 | 0.0010839 | 105.049180 | 0.0578335 | 2 | 3 | heme metabolic process |
| GO:0006955 | 0.0011632 | 2.768018 | 7.0749694 | 16 | 367 | immune response |
| GO:1903900 | 0.0012417 | 7.184664 | 0.8289474 | 5 | 43 | regulation of viral life cycle |
| GO:0051607 | 0.0012629 | 5.711434 | 1.2337821 | 6 | 64 | defense response to virus |
| GO:0010288 | 0.0021408 | 52.508197 | 0.0771114 | 2 | 4 | response to lead ion |
| GO:0060218 | 0.0021408 | 52.508197 | 0.0771114 | 2 | 4 | hematopoietic stem cell differentiation |
| GO:0043903 | 0.0034670 | 5.552428 | 1.0410037 | 5 | 54 | regulation of symbiosis |
| GO:0035455 | 0.0035237 | 34.994535 | 0.0963892 | 2 | 5 | response to interferon-alpha |
| GO:0033013 | 0.0052200 | 26.237705 | 0.1156671 | 2 | 6 | tetrapyrrole metabolic process |
| GO:0045022 | 0.0052200 | 26.237705 | 0.1156671 | 2 | 6 | early endosome to late endosome transport |
| GO:0001676 | 0.0053090 | 9.965625 | 0.3662791 | 3 | 19 | long-chain fatty acid metabolic process |
| GO:0071345 | 0.0055523 | 3.307744 | 2.7567319 | 8 | 143 | cellular response to cytokine stimulus |
| GO:0010970 | 0.0061608 | 9.376471 | 0.3855569 | 3 | 20 | microtubule-based transport |
| GO:0002724 | 0.0072175 | 20.983607 | 0.1349449 | 2 | 7 | regulation of T cell cytokine production |
| GO:0006950 | 0.0083516 | 1.961425 | 16.0006120 | 25 | 830 | response to stress |
1.7 Gene Ontology Analysis of CD8+ T cells
| GOMFID | Pvalue | OddsRatio | ExpCount | Count | Size | Term |
|---|---|---|---|---|---|---|
| GO:0034340 | 0.0000000 | 29.711599 | 0.3162248 | 7 | 40 | response to type I interferon |
| GO:0060337 | 0.0000011 | 35.017241 | 0.1919093 | 5 | 25 | type I interferon signaling pathway |
| GO:0051607 | 0.0000246 | 7.755112 | 1.2095597 | 8 | 153 | defense response to virus |
| GO:0051707 | 0.0000355 | 4.470486 | 3.5180005 | 13 | 445 | response to other organism |
| GO:0045071 | 0.0000397 | 25.405152 | 0.1976405 | 4 | 25 | negative regulation of viral genome replication |
| GO:0009607 | 0.0000525 | 4.291760 | 3.6523960 | 13 | 462 | response to biotic stimulus |
| GO:0008637 | 0.0000806 | 12.988782 | 0.4506203 | 5 | 57 | apoptotic mitochondrial changes |
| GO:0090200 | 0.0001613 | 35.832845 | 0.1106787 | 3 | 14 | positive regulation of release of cytochrome c from mitochondria |
| GO:0050776 | 0.0001712 | 3.780138 | 4.1030163 | 13 | 519 | regulation of immune response |
| GO:2001267 | 0.0002963 | 28.144009 | 0.1343955 | 3 | 17 | regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway |
| GO:0080134 | 0.0003352 | 3.215948 | 5.6208952 | 15 | 711 | regulation of response to stress |
| GO:0045910 | 0.0003655 | 129.444444 | 0.0316225 | 2 | 4 | negative regulation of DNA recombination |
| GO:0006955 | 0.0004375 | 4.546488 | 2.3279347 | 9 | 339 | immune response |
| GO:0044764 | 0.0005071 | 4.019572 | 2.8697397 | 10 | 363 | multi-organism cellular process |
| GO:0048525 | 0.0005332 | 12.090909 | 0.3794697 | 4 | 48 | negative regulation of viral process |
| GO:0034341 | 0.0005619 | 8.308642 | 0.6798832 | 5 | 86 | response to interferon-gamma |
| GO:0006952 | 0.0006269 | 3.154783 | 5.3443114 | 14 | 714 | defense response |
| GO:0002221 | 0.0008437 | 7.554307 | 0.7431282 | 5 | 94 | pattern recognition receptor signaling pathway |
| GO:0045132 | 0.0008478 | 18.746544 | 0.1897349 | 3 | 24 | meiotic chromosome segregation |
| GO:0044419 | 0.0008690 | 3.731350 | 3.0752858 | 10 | 389 | interspecies interaction between organisms |
| GO:0010821 | 0.0012742 | 6.852891 | 0.8142788 | 5 | 103 | regulation of mitochondrion organization |
| GO:0035455 | 0.0016712 | 43.126984 | 0.0632450 | 2 | 8 | response to interferon-alpha |
| GO:0006733 | 0.0018775 | 8.424668 | 0.5296765 | 4 | 67 | oxidoreduction coenzyme metabolic process |
| GO:0060252 | 0.0021377 | 36.961451 | 0.0711506 | 2 | 9 | positive regulation of glial cell proliferation |
| GO:0006839 | 0.0023259 | 5.932153 | 0.9328631 | 5 | 118 | mitochondrial transport |
| GO:0048678 | 0.0023692 | 12.683663 | 0.2687910 | 3 | 34 | response to axon injury |
| GO:0035456 | 0.0026585 | 32.337302 | 0.0790562 | 2 | 10 | response to interferon-beta |
| GO:0002830 | 0.0032328 | 28.740741 | 0.0869618 | 2 | 11 | positive regulation of type 2 immune response |
| GO:0046597 | 0.0032328 | 28.740741 | 0.0869618 | 2 | 11 | negative regulation of viral entry into host cell |
| GO:0050672 | 0.0032657 | 11.228571 | 0.3004135 | 3 | 38 | negative regulation of lymphocyte proliferation |
| GO:0048285 | 0.0034965 | 3.914005 | 1.9843104 | 7 | 251 | organelle fission |
| GO:1903900 | 0.0037528 | 6.880988 | 0.6403551 | 4 | 81 | regulation of viral life cycle |
| GO:0034143 | 0.0038596 | 25.863492 | 0.0948674 | 2 | 12 | regulation of toll-like receptor 4 signaling pathway |
| GO:0097296 | 0.0038596 | 25.863492 | 0.0948674 | 2 | 12 | activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway |
| GO:0007006 | 0.0040578 | 10.338285 | 0.3241304 | 3 | 41 | mitochondrial membrane organization |
| GO:0042176 | 0.0042590 | 4.287329 | 1.5415957 | 6 | 195 | regulation of protein catabolic process |
| GO:0043068 | 0.0044008 | 3.393112 | 2.6246655 | 8 | 332 | positive regulation of programmed cell death |
| GO:0002218 | 0.0044279 | 5.066288 | 1.0830698 | 5 | 137 | activation of innate immune response |
| GO:1902589 | 0.0044799 | 2.312729 | 8.7683657 | 17 | 1157 | single-organism organelle organization |
| GO:0090025 | 0.0045382 | 23.509380 | 0.1027730 | 2 | 13 | regulation of monocyte chemotaxis |
| GO:2000377 | 0.0050479 | 6.302108 | 0.6956945 | 4 | 88 | regulation of reactive oxygen species metabolic process |
| GO:0071345 | 0.0050763 | 3.307969 | 2.6879105 | 8 | 340 | cellular response to cytokine stimulus |
| GO:2000108 | 0.0052677 | 21.547619 | 0.1106787 | 2 | 14 | positive regulation of leukocyte apoptotic process |
| GO:0030260 | 0.0052817 | 9.349078 | 0.3557529 | 3 | 45 | entry into host cell |
| GO:0051828 | 0.0052817 | 9.349078 | 0.3557529 | 3 | 45 | entry into other organism involved in symbiotic interaction |
| GO:0052126 | 0.0052817 | 9.349078 | 0.3557529 | 3 | 45 | movement in host environment |
| GO:0032102 | 0.0054658 | 4.806954 | 1.1384091 | 5 | 144 | negative regulation of response to external stimulus |
| GO:0034138 | 0.0056186 | 9.130533 | 0.3636585 | 3 | 46 | toll-like receptor 3 signaling pathway |
| GO:0009895 | 0.0056846 | 6.082533 | 0.7194113 | 4 | 91 | negative regulation of catabolic process |
| GO:0043123 | 0.0059082 | 6.012668 | 0.7273170 | 4 | 92 | positive regulation of I-kappaB kinase/NF-kappaB signaling |
| GO:0060338 | 0.0060472 | 19.887668 | 0.1185843 | 2 | 15 | regulation of type I interferon-mediated signaling pathway |
| GO:0050727 | 0.0061308 | 4.670163 | 1.1700316 | 5 | 148 | regulation of inflammatory response |
| GO:0031349 | 0.0063777 | 3.925127 | 1.6759912 | 6 | 212 | positive regulation of defense response |
| GO:0042981 | 0.0064414 | 2.443857 | 6.0873267 | 13 | 770 | regulation of apoptotic process |
| GO:0002507 | 0.0068761 | 18.464853 | 0.1264899 | 2 | 16 | tolerance induction |
| GO:0007129 | 0.0068761 | 18.464853 | 0.1264899 | 2 | 16 | synapsis |
| GO:0010939 | 0.0068761 | 18.464853 | 0.1264899 | 2 | 16 | regulation of necrotic cell death |
| GO:0031338 | 0.0068761 | 18.464853 | 0.1264899 | 2 | 16 | regulation of vesicle fusion |
| GO:0006974 | 0.0070974 | 3.407861 | 2.2610071 | 7 | 286 | cellular response to DNA damage stimulus |
| GO:0032103 | 0.0072326 | 4.478747 | 1.2174653 | 5 | 154 | positive regulation of response to external stimulus |
| GO:0016601 | 0.0077534 | 17.231746 | 0.1343955 | 2 | 17 | Rac protein signal transduction |
| GO:0045646 | 0.0077534 | 17.231746 | 0.1343955 | 2 | 17 | regulation of erythrocyte differentiation |
| GO:0000710 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | meiotic mismatch repair |
| GO:0005999 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | xylulose biosynthetic process |
| GO:0009052 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | pentose-phosphate shunt |
| GO:0010266 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | response to vitamin B1 |
| GO:0014739 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of muscle hyperplasia |
| GO:0015747 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | urate transport |
| GO:0034127 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | regulation of MyD88-independent toll-like receptor signaling pathway |
| GO:0034157 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of toll-like receptor 7 signaling pathway |
| GO:0034165 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of toll-like receptor 9 signaling pathway |
| GO:0034276 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | kynurenic acid biosynthetic process |
| GO:0036269 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | swimming behavior |
| GO:0038195 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | urokinase plasminogen activator signaling pathway |
| GO:0042795 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | snRNA transcription from RNA polymerase II promoter |
| GO:0044727 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | DNA demethylation of male pronucleus |
| GO:0048294 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | negative regulation of isotype switching to IgE isotypes |
| GO:0070447 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of oligodendrocyte progenitor proliferation |
| GO:0070667 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | negative regulation of mast cell proliferation |
| GO:0072046 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | establishment of planar polarity involved in nephron morphogenesis |
| GO:0090220 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | chromosome localization to nuclear envelope involved in homologous chromosome segregation |
| GO:0090258 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | negative regulation of mitochondrial fission |
| GO:1900402 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | regulation of carbohydrate metabolic process by regulation of transcription from RNA polymerase II promoter |
| GO:1902616 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | acyl carnitine transmembrane transport |
| GO:1903147 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | negative regulation of mitophagy |
| GO:1903852 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of cristae formation |
| GO:1904379 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | protein localization to cytosolic proteasome complex involved in ERAD pathway |
| GO:1904544 | 0.0079056 | Inf | 0.0079056 | 1 | 1 | positive regulation of free ubiquitin chain polymerization |
| GO:0007059 | 0.0079113 | 5.506147 | 0.7905619 | 4 | 100 | chromosome segregation |
| GO:0050869 | 0.0086783 | 16.152778 | 0.1423011 | 2 | 18 | negative regulation of B cell activation |
| GO:0001817 | 0.0092878 | 3.227832 | 2.3795913 | 7 | 301 | regulation of cytokine production |
| GO:0051603 | 0.0093687 | 3.601544 | 1.8182924 | 6 | 230 | proteolysis involved in cellular protein catabolic process |
| GO:0050863 | 0.0096005 | 4.165104 | 1.3044271 | 5 | 165 | regulation of T cell activation |
| GO:0043903 | 0.0096766 | 5.178399 | 0.8379956 | 4 | 106 | regulation of symbiosis |
| GO:0051716 | 0.0098518 | 1.852192 | 29.1638288 | 39 | 3689 | cellular response to stimulus |
2 Part 1: MethylTarget Technology Evaluation and Quality Control
2.1 Quality Control:The average coverage of each sample, each CpGsite, and each gene (average coverage of the CpGsites in a gene)
2.1.1 Table 1: The Average Missing Rate of Each Sample
| Sample | Missing.Rate | |
|---|---|---|
| D10 | D10 | 0.173 |
| D11 | D11 | 0.173 |
| D12 | D12 | 0.132 |
| D13 | D13 | 0.173 |
| D14 | D14 | 0.173 |
| D15 | D15 | 0.173 |
| D1 | D1 | 0.173 |
| D2 | D2 | 0.173 |
| D3 | D3 | 0.173 |
| D4 | D4 | 0.173 |
| D5 | D5 | 0.173 |
| D6 | D6 | 0.173 |
| D7 | D7 | 0.173 |
| D8 | D8 | 0.132 |
| D9 | D9 | 0.173 |
| MS001 | MS001 | 0.132 |
| MS002 | MS002 | 0.148 |
| MS003 | MS003 | 0.132 |
| MS004 | MS004 | 0.132 |
| MS005 | MS005 | 0.132 |
| MS006 | MS006 | 0.132 |
| MS007 | MS007 | 0.132 |
| MS008 | MS008 | 0.132 |
| MS009 | MS009 | 0.132 |
| MS010 | MS010 | 0.132 |
| MS011 | MS011 | 0.136 |
| MS012 | MS012 | 0.132 |
| MS013 | MS013 | 0.132 |
| MS014 | MS014 | 0.136 |
| MS015 | MS015 | 0.169 |
| MS016 | MS016 | 0.148 |
| MS017 | MS017 | 0.169 |
| MS018 | MS018 | 0.132 |
| MS019 | MS019 | 0.132 |
| MS020 | MS020 | 0.132 |
| MS021 | MS021 | 0.132 |
| MS022 | MS022 | 0.132 |
| MS023 | MS023 | 0.132 |
| MS024 | MS024 | 0.000 |
| MS025 | MS025 | 0.132 |
| MS026 | MS026 | 0.132 |
| MS027 | MS027 | 0.132 |
| MS028 | MS028 | 0.132 |
| MS029 | MS029 | 0.132 |
| MS030 | MS030 | 0.132 |
| MS031 | MS031 | 0.132 |
| MS032 | MS032 | 0.132 |
| MS033 | MS033 | 0.132 |
| MS034 | MS034 | 0.132 |
| MS035 | MS035 | 0.132 |
| MS036 | MS036 | 0.132 |
| MS037 | MS037 | 0.132 |
| MS038 | MS038 | 0.132 |
| MS039 | MS039 | 0.193 |
| MS040 | MS040 | 0.132 |
| MS041 | MS041 | 0.152 |
| MS042 | MS042 | 0.132 |
| MS043 | MS043 | 0.132 |
| MS044 | MS044 | 0.148 |
| MS045 | MS045 | 0.132 |
| MS046 | MS046 | 0.140 |
| MS047 | MS047 | 0.165 |
| MS048 | MS048 | 0.132 |
| MS049 | MS049 | 0.132 |
| MS050 | MS050 | 0.132 |
| MS051 | MS051 | 0.136 |
| MS052 | MS052 | 0.132 |
| MS053 | MS053 | 0.132 |
| MS054 | MS054 | 0.148 |
| MS055 | MS055 | 0.132 |
| MS056 | MS056 | 0.169 |
| MS057 | MS057 | 0.132 |
| MS058 | MS058 | 0.148 |
| MS059 | MS059 | 0.132 |
| MS060 | MS060 | 0.132 |
| MS061 | MS061 | 0.132 |
| MS062 | MS062 | 0.000 |
| MS063 | MS063 | 0.132 |
| MS064 | MS064 | 0.132 |
| MS065 | MS065 | 0.132 |
| MS066 | MS066 | 0.132 |
| MS067 | MS067 | 0.214 |
| MS068 | MS068 | 0.132 |
| MS069 | MS069 | 0.132 |
| MS070 | MS070 | 0.165 |
| MS071 | MS071 | 0.132 |
| MS072 | MS072 | 0.486 |
| MS073 | MS073 | 0.132 |
| MS074 | MS074 | 0.132 |
| MS075 | MS075 | 0.132 |
| MS076 | MS076 | 0.132 |
| MS077 | MS077 | 0.148 |
| MS078 | MS078 | 0.132 |
| MS079 | MS079 | 0.132 |
| MS080 | MS080 | 0.136 |
| MS081 | MS081 | 0.148 |
| MS082 | MS082 | 0.156 |
| MS083 | MS083 | 0.169 |
| MS084 | MS084 | 0.132 |
| MS085 | MS085 | 0.132 |
| MS086 | MS086 | 0.132 |
| MS087 | MS087 | 0.276 |
| MS088 | MS088 | 0.132 |
| MS089 | MS089 | 0.132 |
| MS090 | MS090 | 0.132 |
| MS091 | MS091 | 0.132 |
| MS092 | MS092 | 0.132 |
| MS093 | MS093 | 0.144 |
| MS094 | MS094 | 0.136 |
| MS095 | MS095 | 0.132 |
| MS096 | MS096 | 0.148 |
| MS097 | MS097 | 0.132 |
| MS098 | MS098 | 0.119 |
| MS099 | MS099 | 0.169 |
| MS100 | MS100 | 0.136 |
| MS101 | MS101 | 0.136 |
| MS102 | MS102 | 0.148 |
| MS103 | MS103 | 0.132 |
| MS104 | MS104 | 0.588 |
| MS105 | MS105 | 0.136 |
| MS106 | MS106 | 0.132 |
| MS107 | MS107 | 0.132 |
| MS108 | MS108 | 0.218 |
| MS109 | MS109 | 0.132 |
| MS110 | MS110 | 0.132 |
| MS111 | MS111 | 0.132 |
| MS112 | MS112 | 0.132 |
| MS113 | MS113 | 0.132 |
| MS114 | MS114 | 0.132 |
| MS115 | MS115 | 0.148 |
| MS116 | MS116 | 0.251 |
| MS117 | MS117 | 0.136 |
| MS118 | MS118 | 0.132 |
| MS119 | MS119 | 0.136 |
| MS120 | MS120 | 0.132 |
| MS121 | MS121 | 0.136 |
| MS122 | MS122 | 0.132 |
| MS123 | MS123 | 0.218 |
| MS124 | MS124 | 0.440 |
| MS125 | MS125 | 0.132 |
| MS126 | MS126 | 0.140 |
| MS127 | MS127 | 0.132 |
| MS128 | MS128 | 0.132 |
| MS129 | MS129 | 0.132 |
| MS130 | MS130 | 0.132 |
| MS131 | MS131 | 0.132 |
| MS132 | MS132 | 0.132 |
| MS133 | MS133 | 0.132 |
| MS134 | MS134 | 0.132 |
| MS135 | MS135 | 0.132 |
| MS136 | MS136 | 0.144 |
| MS137 | MS137 | 0.132 |
| MS138 | MS138 | 0.132 |
| MS139 | MS139 | 0.132 |
| MS140 | MS140 | 0.132 |
| MS141 | MS141 | 0.132 |
| MS142 | MS142 | 0.148 |
| MS143 | MS143 | 0.132 |
| MS144 | MS144 | 0.132 |
| MS145 | MS145 | 0.132 |
| MS146 | MS146 | 0.148 |
| MS147 | MS147 | 0.136 |
| MS148 | MS148 | 0.136 |
| MS149 | MS149 | 0.132 |
| MS150 | MS150 | 0.136 |
| MS151 | MS151 | 0.251 |
| MS152 | MS152 | 0.140 |
| MS153 | MS153 | 0.148 |
| MS154 | MS154 | 0.132 |
| MS155 | MS155 | 0.132 |
| MS156 | MS156 | 0.132 |
| MS157 | MS157 | 0.144 |
| MS158 | MS158 | 0.251 |
| MS159 | MS159 | 0.132 |
| MS160 | MS160 | 0.132 |
| MS161 | MS161 | 0.140 |
| MS162 | MS162 | 0.235 |
| MS163 | MS163 | 0.202 |
| MS164 | MS164 | 0.185 |
2.1.2 Table 2: The Average Coverage of Each CpGsite
| Gene | Total.CpG | Avg.Coverage |
|---|---|---|
| MX1 | 42798695 | 1617.089385 |
| MX1 | 42798698 | 1617.100559 |
| MX1 | 42798723 | 1617.117318 |
| MX1 | 42798733 | 1617.111732 |
| MX1 | 42798747 | 1617.737430 |
| MX1 | 42798749 | 1618.491620 |
| MX1 | 42798765 | 1623.603352 |
| MX1 | 42798781 | 1623.675978 |
| MX1 | 42798813 | 1620.921788 |
| MX1 | 42798816 | 1619.284916 |
| MX1 | 42798818 | 1618.072626 |
| MX1 | 42798829 | 1617.100559 |
| MX1 | 42798837 | 1617.100559 |
| MX1 | 42798847 | 1617.089385 |
| MX1 | 42798857 | 1617.083799 |
| MX1 | 42798863 | 1617.061453 |
| CCDC85C | 100069535 | 2.308943 |
| CCDC85C | 100069538 | 2.308943 |
| CCDC85C | 100069541 | 2.308943 |
| CCDC85C | 100069544 | 2.308943 |
| CCDC85C | 100069552 | 2.317073 |
| CCDC85C | 100069563 | 2.317073 |
| CCDC85C | 100069566 | 2.317073 |
| CCDC85C | 100069585 | 2.325203 |
| CCDC85C | 100069588 | 2.325203 |
| CCDC85C | 100069601 | 2.325203 |
| CCDC85C | 100069606 | 2.325203 |
| CCDC85C | 100069619 | 2.365854 |
| CCDC85C | 100069630 | 2.782258 |
| CCDC85C | 100069645 | 2.801587 |
| CCDC85C | 100069654 | 2.547619 |
| CCDC85C | 100069657 | 2.357143 |
| CCDC85C | 100069664 | 2.349206 |
| CCDC85C | 100069666 | 2.349206 |
| CCDC85C | 100069673 | 2.349206 |
| CCDC85C | 100069684 | 2.349206 |
| CCDC85C | 100069687 | 2.349206 |
| CCDC85C | 100069693 | 2.349206 |
| CCDC85C | 100069696 | 2.349206 |
| CCDC85C | 100069698 | 2.349206 |
| CCDC85C | 100069706 | 2.349206 |
| CCDC85C | 100069708 | 2.349206 |
| CCDC85C | 100069711 | 2.349206 |
| CCDC85C | 100069715 | 2.349206 |
| CCDC85C | 100069717 | 2.349206 |
| CCDC85C | 100069724 | 2.349206 |
| CCDC85C | 100069730 | 2.349206 |
| CCDC85C | 100069735 | 2.349206 |
| RNF39 | 30039123 | 210.497207 |
| RNF39 | 30039127 | 210.709497 |
| RNF39 | 30039130 | 210.804469 |
| RNF39 | 30039132 | 210.860335 |
| RNF39 | 30039142 | 210.921788 |
| RNF39 | 30039151 | 210.927374 |
| RNF39 | 30039158 | 210.932961 |
| RNF39 | 30039175 | 210.944134 |
| RNF39 | 30039186 | 210.938547 |
| RNF39 | 30039202 | 210.938547 |
| RNF39 | 30039206 | 210.932961 |
| RNF39 | 30039208 | 210.944134 |
| RNF39 | 30039232 | 210.463687 |
| RNF39 | 30039235 | 209.972067 |
| RNF39 | 30039239 | 209.703911 |
| COX7A2 | 75953821 | 2134.955056 |
| COX7A2 | 75953829 | 2134.966292 |
| COX7A2 | 75953853 | 2134.966292 |
| COX7A2 | 75953883 | 2140.500000 |
| COX7A2 | 75953935 | 2135.028090 |
| COX7A2 | 75953937 | 2135.000000 |
| COX7A2 | 75953960 | 2134.983146 |
| COX7A2 | 75953974 | 2134.983146 |
| SMAD3 | 67361773 | 126.500000 |
| SMAD3 | 67361798 | 126.516854 |
| SMAD3 | 67361821 | 126.741573 |
| SMAD3 | 67361896 | 126.511236 |
| HLA-DPB1 | 33048286 | 965.536313 |
| HLA-DPB1 | 33048291 | 965.541899 |
| HLA-DPB1 | 33048310 | 965.558659 |
| HLA-DPB1 | 33048370 | 965.547486 |
| RNF39 | 30039271 | 155.005587 |
| RNF39 | 30039274 | 155.000000 |
| RNF39 | 30039278 | 155.000000 |
| RNF39 | 30039303 | 155.000000 |
| RNF39 | 30039307 | 155.000000 |
| RNF39 | 30039313 | 155.000000 |
| RNF39 | 30039323 | 155.000000 |
| RNF39 | 30039349 | 154.988827 |
| RNF39 | 30039354 | 155.273743 |
| RNF39 | 30039364 | 155.798883 |
| RNF39 | 30039374 | 155.877095 |
| RNF39 | 30039376 | 155.871508 |
| RNF39 | 30039380 | 155.843575 |
| RNF39 | 30039403 | 154.949721 |
| RNF39 | 30039408 | 154.983240 |
| RNF39 | 30039411 | 154.949721 |
| RNF39 | 30039415 | 154.955307 |
| RNF39 | 30039418 | 154.949721 |
| RNF39 | 30039432 | 154.955307 |
| RNF39 | 30039435 | 154.960894 |
| RNF39 | 30039442 | 154.949721 |
| RNF39 | 30039466 | 154.949721 |
| RNF39 | 30039476 | 154.698324 |
| TTC39C | 21572657 | 6267.117318 |
| TTC39C | 21572635 | 6267.000000 |
| TTC39C | 21572623 | 6266.988827 |
| IFITM1 | 313354 | 302.402235 |
| IFITM1 | 313408 | 302.340782 |
| HOOK2 | 12877099 | 1991.089385 |
| HOOK2 | 12877107 | 1991.089385 |
| HOOK2 | 12877138 | 1991.167598 |
| HOOK2 | 12877188 | 2003.675978 |
| HOOK2 | 12877201 | 2003.648045 |
| HOOK2 | 12877215 | 1991.396648 |
| HOOK2 | 12877235 | 1990.960894 |
| HOOK2 | 12877276 | 1990.899441 |
| PARP9 | 122281939 | 1402.916201 |
| PARP9 | 122281975 | 1403.078212 |
| BRDT | 92414650 | 272.357542 |
| BRDT | 92414661 | 272.357542 |
| BRDT | 92414719 | 273.089385 |
| BRDT | 92414722 | 273.072626 |
| BRDT | 92414737 | 273.072626 |
| BRDT | 92414751 | 273.016760 |
| BRDT | 92414770 | 272.379888 |
| BRDT | 92414782 | 272.379888 |
| BRDT | 92414793 | 272.379888 |
| COX7A2 | 75954022 | 466.061452 |
| COX7A2 | 75954053 | 466.111732 |
| COX7A2 | 75954118 | 466.044693 |
| COX7A2 | 75954122 | 465.977654 |
| HELZ2 | 62199034 | 118.670455 |
| HELZ2 | 62199061 | 118.670455 |
| HELZ2 | 62199156 | 118.676136 |
| HELZ2 | 62199181 | 118.676136 |
| HELZ2 | 62199190 | 118.670455 |
| GFPT2 | 179741121 | 795.642458 |
| GFPT2 | 179741105 | 796.826816 |
| GFPT2 | 179741101 | 797.603352 |
| GFPT2 | 179741081 | 795.843575 |
| GFPT2 | 179741067 | 795.921788 |
| GFPT2 | 179741063 | 795.793296 |
| GFPT2 | 179741060 | 795.793296 |
| GFPT2 | 179741042 | 745.469274 |
| GFPT2 | 179741039 | 718.039106 |
| EIF2AK2 | 37383568 | 1496.245810 |
| EIF2AK2 | 37383588 | 1496.279330 |
| EIF2AK2 | 37383623 | 1498.664804 |
| EIF2AK2 | 37383679 | 1496.301676 |
| EIF2AK2 | 37383713 | 1496.318436 |
| EIF2AK2 | 37383730 | 1496.318436 |
| TLR1 | 38805732 | 33.642046 |
| TLR1 | 38805839 | 33.653409 |
| HOOK2 | 12877020 | 5503.972067 |
| HOOK2 | 12877001 | 5545.195531 |
| HOOK2 | 12876997 | 5545.642458 |
| HOOK2 | 12876993 | 5545.178771 |
| HOOK2 | 12876987 | 5545.162011 |
| HOOK2 | 12876969 | 5545.167598 |
| HOOK2 | 12876948 | 5547.832402 |
| HOOK2 | 12876946 | 5545.245810 |
| HOOK2 | 12876944 | 5545.167598 |
| HOOK2 | 12876942 | 5545.229050 |
| HOOK2 | 12876937 | 5545.178771 |
| HOOK2 | 12876926 | 5542.759777 |
| HOOK2 | 12876918 | 5534.843575 |
| HOOK2 | 12876911 | 5508.072626 |
| GFPT2 | 179741008 | 1613.100559 |
| GFPT2 | 179740999 | 1613.815642 |
| GFPT2 | 179740994 | 1613.821229 |
| GFPT2 | 179740992 | 1613.826816 |
| GFPT2 | 179740970 | 1613.821229 |
| GFPT2 | 179740963 | 1613.821229 |
| GFPT2 | 179740957 | 1613.826816 |
| GFPT2 | 179740955 | 1613.832402 |
| GFPT2 | 179740940 | 1615.620112 |
| GFPT2 | 179740935 | 1615.893855 |
| GFPT2 | 179740920 | 1616.173184 |
| GFPT2 | 179740918 | 1616.184358 |
| GFPT2 | 179740915 | 1616.162011 |
| GFPT2 | 179740906 | 1616.178771 |
| GFPT2 | 179740900 | 1616.117318 |
| GFPT2 | 179740888 | 1615.368715 |
| GFPT2 | 179740869 | 1613.854749 |
| GFPT2 | 179740867 | 1613.810056 |
| GFPT2 | 179740861 | 1613.815642 |
| GFPT2 | 179740855 | 1613.893855 |
| GFPT2 | 179740852 | 1613.815642 |
| GFPT2 | 179740840 | 1613.798883 |
| GFPT2 | 179740832 | 1613.793296 |
| GFPT2 | 179740825 | 1613.854749 |
| GFPT2 | 179740822 | 1613.804469 |
| FAM132A | 1178246 | 634.519553 |
| FAM132A | 1178207 | 634.614525 |
| FAM132A | 1178202 | 635.653631 |
| FAM132A | 1178192 | 636.011173 |
| FAM132A | 1178182 | 636.329609 |
| FAM132A | 1178172 | 636.363129 |
| FAM132A | 1178162 | 635.748603 |
| FAM132A | 1178150 | 634.832402 |
| FAM132A | 1178136 | 634.832402 |
| FAM132A | 1178118 | 634.837989 |
| FAM132A | 1178105 | 634.843575 |
| FAM132A | 1178086 | 634.832402 |
| BRDT | 92417998 | 722.083799 |
| BRDT | 92418017 | 722.078212 |
| HLA-DPB1 | 33048417 | 273.307263 |
| HLA-DPB1 | 33048423 | 273.312849 |
| HLA-DPB1 | 33048433 | 273.318436 |
| HLA-DPB1 | 33048444 | 273.351955 |
| HLA-DPB1 | 33048469 | 273.324022 |
| HLA-DPB1 | 33048483 | 273.513966 |
| HLA-DPB1 | 33048485 | 273.625698 |
| HLA-DPB1 | 33048502 | 274.798883 |
| HLA-DPB1 | 33048529 | 274.089385 |
| HLA-DPB1 | 33048540 | 273.329609 |
| HLA-DPB1 | 33048542 | 273.324022 |
| HLA-DPB1 | 33048544 | 273.324022 |
| HLA-DPB1 | 33048549 | 273.324022 |
| HLA-DPB1 | 33048555 | 273.324022 |
| HLA-DPB1 | 33048558 | 273.324022 |
| HLA-DPB1 | 33048571 | 273.346369 |
| HLA-DPB1 | 33048575 | 273.329609 |
| HLA-DPB1 | 33048581 | 273.312849 |
| HLA-DPB1 | 33048592 | 273.318436 |
| HLA-DPB1 | 33048602 | 273.307263 |
| IFI44L | 79085586 | 465.646067 |
| IFI44L | 79085647 | 465.646067 |
| IFI44L | 79085713 | 465.640449 |
| IFI44L | 79085765 | 465.640449 |
| IFITM1 | 312419 | 71.934524 |
| IFITM1 | 312434 | 74.345238 |
| IFITM1 | 312463 | 85.023809 |
| IFITM1 | 312518 | 57.890909 |
| UPK3B | 76145717 | 831.505882 |
| UPK3B | 76145702 | 832.070588 |
| UPK3B | 76145693 | 834.358823 |
| UPK3B | 76145689 | 834.741177 |
| UPK3B | 76145673 | 835.000000 |
| UPK3B | 76145633 | 834.988235 |
| UPK3B | 76145628 | 834.988235 |
| UPK3B | 76145620 | 834.982353 |
| UPK3B | 76145606 | 834.982353 |
| UPK3B | 76145589 | 832.070588 |
| ###Table 3: | The Average C | overage of Each Gene |
| Gene | Average Coverage of Gene | |
|---|---|---|
| 2 | CCDC85C | 2.372799 |
| 16 | TLR1 | 33.647727 |
| 7 | HELZ2 | 118.672727 |
| 15 | SMAD3 | 126.567416 |
| 11 | IFITM1 | 148.989583 |
| 14 | RNF39 | 177.064540 |
| 1 | BRDT | 354.388014 |
| 8 | HLA-DPB1 | 388.807961 |
| 10 | IFI44L | 465.643258 |
| 5 | FAM132A | 635.284916 |
| 18 | UPK3B | 833.968823 |
| 6 | GFPT2 | 1394.086428 |
| 13 | PARP9 | 1402.997207 |
| 4 | EIF2AK2 | 1496.688082 |
| 3 | COX7A2 | 1579.131463 |
| 12 | MX1 | 1618.477654 |
| 9 | HOOK2 | 4249.935246 |
| 17 | TTC39C | 6267.035382 |
2.2 Correlation of MethylTarget Technology and Methylation 450K technology with same samples and same CpGsites in CD4+/CD8+
2.2.1 Table 4: The Correlation of each CpGsite between two techniques in CD4+ and CD8+ T cells
| CpGsites | Position | Gene | Cor | Cor.p | |
|---|---|---|---|---|---|
| cg08924203 | cg08924203 | 42798747 | MX1 | 0.7875911 | 0.0000000 |
| cg09234582 | cg09234582 | 33048286 | HLA-DPB1 | 0.8329984 | 0.0000000 |
| cg25045942 | cg25045942 | 33048291 | HLA-DPB1 | 0.8769142 | 0.0000000 |
| cg13349035 | cg13349035 | 33048310 | HLA-DPB1 | 0.8813230 | 0.0000000 |
| cg24961286 | cg24961286 | 67361773 | SMAD3 | 0.9302960 | 0.0000000 |
| cg06809298 | cg06809298 | 75953853 | COX7A2 | 0.9400949 | 0.0000000 |
| cg19367436 | cg19367436 | 75953935 | COX7A2 | 0.8163266 | 0.0000000 |
| cg00947782 | cg00947782 | 30039142 | RNF39 | 0.5845140 | 0.0000103 |
| cg18930910 | cg18930910 | 30039151 | RNF39 | 0.5916786 | 0.0000076 |
| cg03343571 | cg03343571 | 30039175 | RNF39 | 0.5276578 | 0.0000978 |
| cg20249327 | cg20249327 | 30039374 | RNF39 | 0.9220030 | 0.0000000 |
| cg15877520 | cg15877520 | 30039376 | RNF39 | 0.9296247 | 0.0000000 |
| cg13918754 | cg13918754 | 30039380 | RNF39 | 0.9596576 | 0.0000000 |
| cg09279736 | cg09279736 | 30039403 | RNF39 | 0.9135974 | 0.0000000 |
| cg07382347 | cg07382347 | 30039408 | RNF39 | 0.9166788 | 0.0000000 |
| cg13401893 | cg13401893 | 30039432 | RNF39 | 0.9084653 | 0.0000000 |
| cg12633154 | cg12633154 | 30039435 | RNF39 | 0.8883291 | 0.0000000 |
| cg10568066 | cg10568066 | 30039442 | RNF39 | 0.8677459 | 0.0000000 |
| cg16078649 | cg16078649 | 30039466 | RNF39 | 0.9190687 | 0.0000000 |
| cg10930308 | cg10930308 | 30039476 | RNF39 | 0.9493699 | 0.0000000 |
| cg11694510 | cg11694510 | 313354 | IFITM1 | 0.7864492 | 0.0000000 |
| cg23899408 | cg23899408 | 12877188 | HOOK2 | 0.9765644 | 0.0000000 |
| cg14732540 | cg14732540 | 92414722 | BRDT | 0.8713379 | 0.0000000 |
| cg13299824 | cg13299824 | 92414737 | BRDT | 0.8400119 | 0.0000000 |
| cg02935097 | cg02935097 | 92414782 | BRDT | 0.7988980 | 0.0000000 |
| cg08122652 | cg08122652 | 122281939 | PARP9 | 0.7637794 | 0.0000000 |
| cg00959259 | cg00959259 | 122281975 | PARP9 | 0.6588623 | 0.0000003 |
| cg25716013 | cg25716013 | 75954053 | COX7A2 | 0.9095258 | 0.0000000 |
| cg17593958 | cg17593958 | 62199034 | HELZ2 | 0.8444909 | 0.0000000 |
| cg11779113 | cg11779113 | 62199156 | HELZ2 | 0.4249446 | 0.0040367 |
| cg06064964 | cg06064964 | 62199181 | HELZ2 | 0.7381923 | 0.0000000 |
| cg09844573 | cg09844573 | 62199190 | HELZ2 | 0.6197099 | 0.0000073 |
| cg17326313 | cg17326313 | 37383568 | EIF2AK2 | 0.8792872 | 0.0000000 |
| cg02016764 | cg02016764 | 38805732 | TLR1 | 0.7114730 | 0.0000008 |
| cg01081438 | cg01081438 | 92417998 | BRDT | 0.9337179 | 0.0000000 |
| cg10850215 | cg10850215 | 33048469 | HLA-DPB1 | 0.6474086 | 0.0000007 |
| cg03229061 | cg03229061 | 33048483 | HLA-DPB1 | 0.4858796 | 0.0004636 |
| cg17588455 | cg17588455 | 33048485 | HLA-DPB1 | 0.7545157 | 0.0000000 |
| cg26645432 | cg26645432 | 33048502 | HLA-DPB1 | 0.1232234 | 0.4040559 |
| cg06437840 | cg06437840 | 33048529 | HLA-DPB1 | 0.7110659 | 0.0000000 |
| cg14870156 | cg14870156 | 33048540 | HLA-DPB1 | 0.0343315 | 0.8168069 |
| cg19990651 | cg19990651 | 33048555 | HLA-DPB1 | 0.7052687 | 0.0000000 |
| cg01132696 | cg01132696 | 33048558 | HLA-DPB1 | 0.3265685 | 0.0234882 |
| cg03607951 | cg03607951 | 79085586 | IFI44L | 0.6966504 | 0.0000000 |
| cg17980508 | cg17980508 | 79085713 | IFI44L | 0.6256915 | 0.0000020 |
| cg00855901 | cg00855901 | 79085765 | IFI44L | 0.7205904 | 0.0000000 |
| cg05432003 | cg05432003 | 312518 | IFITM1 | 0.0566625 | 0.8022332 |
| cg05372444 | cg05372444 | 76145673 | UPK3B | 0.0945557 | 0.5181153 |
| cg16453056 | cg16453056 | 76145633 | UPK3B | -0.0627056 | 0.6686297 |
| cg18719665 | cg18719665 | 21572657 | TTC39C | 0.7129571 | 0.0000000 |
| cg05401069 | cg05401069 | 21572635 | TTC39C | 0.7021158 | 0.0000000 |
| cg12639429 | cg12639429 | 21572623 | TTC39C | 0.7214840 | 0.0000000 |
| cg02891314 | cg02891314 | 179741121 | GFPT2 | 0.9772109 | 0.0000000 |
| cg23248424 | cg23248424 | 179741105 | GFPT2 | 0.9740999 | 0.0000000 |
| cg11738485 | cg11738485 | 12877001 | HOOK2 | 0.9661724 | 0.0000000 |
| cg13944838 | cg13944838 | 179740915 | GFPT2 | 0.9192473 | 0.0000000 |
| cg24345856 | cg24345856 | 1178246 | FAM132A | 0.9772829 | 0.0000000 |
2.2.2 Table 5: The Correlation of each CpGsite between two techniques in CD4+ T cells
| CpGsites | Gene | Cor | Cor.p | |
|---|---|---|---|---|
| cg08924203 | cg08924203 | MX1 | 0.8299157 | 0.0000003 |
| cg09234582 | cg09234582 | HLA-DPB1 | 0.8654015 | 0.0000000 |
| cg25045942 | cg25045942 | HLA-DPB1 | 0.8925666 | 0.0000000 |
| cg13349035 | cg13349035 | HLA-DPB1 | 0.9083435 | 0.0000000 |
| cg24961286 | cg24961286 | SMAD3 | 0.9460214 | 0.0000000 |
| cg06809298 | cg06809298 | COX7A2 | 0.9589386 | 0.0000000 |
| cg19367436 | cg19367436 | COX7A2 | 0.8566601 | 0.0000001 |
| cg00947782 | cg00947782 | RNF39 | 0.6241475 | 0.0008548 |
| cg18930910 | cg18930910 | RNF39 | 0.5285853 | 0.0065991 |
| cg03343571 | cg03343571 | RNF39 | 0.5337884 | 0.0059928 |
| cg20249327 | cg20249327 | RNF39 | 0.9182796 | 0.0000000 |
| cg15877520 | cg15877520 | RNF39 | 0.9374247 | 0.0000000 |
| cg13918754 | cg13918754 | RNF39 | 0.9548662 | 0.0000000 |
| cg09279736 | cg09279736 | RNF39 | 0.9228781 | 0.0000000 |
| cg07382347 | cg07382347 | RNF39 | 0.9244311 | 0.0000000 |
| cg13401893 | cg13401893 | RNF39 | 0.9082009 | 0.0000000 |
| cg12633154 | cg12633154 | RNF39 | 0.9102277 | 0.0000000 |
| cg10568066 | cg10568066 | RNF39 | 0.8987335 | 0.0000000 |
| cg16078649 | cg16078649 | RNF39 | 0.9467700 | 0.0000000 |
| cg10930308 | cg10930308 | RNF39 | 0.9551814 | 0.0000000 |
| cg11694510 | cg11694510 | IFITM1 | 0.7563685 | 0.0000122 |
| cg23899408 | cg23899408 | HOOK2 | 0.9775041 | 0.0000000 |
| cg14732540 | cg14732540 | BRDT | 0.8203313 | 0.0000005 |
| cg13299824 | cg13299824 | BRDT | 0.8513942 | 0.0000001 |
| cg02935097 | cg02935097 | BRDT | 0.8637596 | 0.0000000 |
| cg08122652 | cg08122652 | PARP9 | 0.7920321 | 0.0000024 |
| cg00959259 | cg00959259 | PARP9 | 0.7744853 | 0.0000055 |
| cg25716013 | cg25716013 | COX7A2 | 0.8931213 | 0.0000000 |
| cg17593958 | cg17593958 | HELZ2 | 0.7961157 | 0.0000158 |
| cg11779113 | cg11779113 | HELZ2 | 0.3829578 | 0.0866200 |
| cg06064964 | cg06064964 | HELZ2 | 0.7340518 | 0.0001519 |
| cg09844573 | cg09844573 | HELZ2 | 0.6369182 | 0.0019033 |
| cg17326313 | cg17326313 | EIF2AK2 | 0.9105197 | 0.0000000 |
| cg02016764 | cg02016764 | TLR1 | 0.6434139 | 0.0006942 |
| cg01081438 | cg01081438 | BRDT | 0.9408440 | 0.0000000 |
| cg10850215 | cg10850215 | HLA-DPB1 | 0.7368557 | 0.0000266 |
| cg03229061 | cg03229061 | HLA-DPB1 | 0.4504181 | 0.0238546 |
| cg17588455 | cg17588455 | HLA-DPB1 | 0.8114746 | 0.0000009 |
| cg26645432 | cg26645432 | HLA-DPB1 | 0.2312224 | 0.2661047 |
| cg06437840 | cg06437840 | HLA-DPB1 | 0.7226194 | 0.0000451 |
| cg14870156 | cg14870156 | HLA-DPB1 | -0.0263505 | 0.9005009 |
| cg19990651 | cg19990651 | HLA-DPB1 | 0.7628868 | 0.0000092 |
| cg01132696 | cg01132696 | HLA-DPB1 | 0.2636762 | 0.2028171 |
| cg03607951 | cg03607951 | IFI44L | 0.5938188 | 0.0022188 |
| cg17980508 | cg17980508 | IFI44L | 0.4851683 | 0.0162569 |
| cg00855901 | cg00855901 | IFI44L | 0.5496102 | 0.0054020 |
| cg05432003 | cg05432003 | IFITM1 | 0.2915337 | 0.4835571 |
| cg05372444 | cg05372444 | UPK3B | 0.1231249 | 0.5576437 |
| cg16453056 | cg16453056 | UPK3B | -0.1314347 | 0.5311479 |
| cg18719665 | cg18719665 | TTC39C | 0.7752723 | 0.0000053 |
| cg05401069 | cg05401069 | TTC39C | 0.8837758 | 0.0000000 |
| cg12639429 | cg12639429 | TTC39C | 0.8685243 | 0.0000000 |
| cg02891314 | cg02891314 | GFPT2 | 0.9830951 | 0.0000000 |
| cg23248424 | cg23248424 | GFPT2 | 0.9803569 | 0.0000000 |
| cg11738485 | cg11738485 | HOOK2 | 0.9654121 | 0.0000000 |
| cg13944838 | cg13944838 | GFPT2 | 0.9162778 | 0.0000000 |
| cg24345856 | cg24345856 | FAM132A | 0.9758109 | 0.0000000 |
2.2.3 Table 6: The Correlation of each CpGsite between two techniques in CD8+ T cells
| CpGsites | Gene | Cor | Cor.p | |
|---|---|---|---|---|
| cg08924203 | cg08924203 | MX1 | 0.8415787 | 0.0000001 |
| cg00947782 | cg00947782 | RNF39 | 0.6452495 | 0.0006624 |
| cg18930910 | cg18930910 | RNF39 | 0.6936552 | 0.0001707 |
| cg03343571 | cg03343571 | RNF39 | 0.6162826 | 0.0013425 |
| cg09234582 | cg09234582 | HLA-DPB1 | 0.7949194 | 0.0000021 |
| cg25045942 | cg25045942 | HLA-DPB1 | 0.8763508 | 0.0000000 |
| cg13349035 | cg13349035 | HLA-DPB1 | 0.8666077 | 0.0000000 |
| cg06809298 | cg06809298 | COX7A2 | 0.9425910 | 0.0000000 |
| cg19367436 | cg19367436 | COX7A2 | 0.8157639 | 0.0000012 |
| cg20249327 | cg20249327 | RNF39 | 0.9287367 | 0.0000000 |
| cg15877520 | cg15877520 | RNF39 | 0.9228730 | 0.0000000 |
| cg13918754 | cg13918754 | RNF39 | 0.9738624 | 0.0000000 |
| cg09279736 | cg09279736 | RNF39 | 0.9528922 | 0.0000000 |
| cg07382347 | cg07382347 | RNF39 | 0.9573280 | 0.0000000 |
| cg13401893 | cg13401893 | RNF39 | 0.9167430 | 0.0000000 |
| cg12633154 | cg12633154 | RNF39 | 0.8927020 | 0.0000000 |
| cg10568066 | cg10568066 | RNF39 | 0.8855962 | 0.0000000 |
| cg16078649 | cg16078649 | RNF39 | 0.9116806 | 0.0000000 |
| cg10930308 | cg10930308 | RNF39 | 0.9483145 | 0.0000000 |
| cg11694510 | cg11694510 | IFITM1 | 0.8453997 | 0.0000002 |
| cg23899408 | cg23899408 | HOOK2 | 0.9768685 | 0.0000000 |
| cg25716013 | cg25716013 | COX7A2 | 0.9555204 | 0.0000000 |
| cg14732540 | cg14732540 | BRDT | 0.9358410 | 0.0000000 |
| cg13299824 | cg13299824 | BRDT | 0.9490383 | 0.0000000 |
| cg02935097 | cg02935097 | BRDT | 0.9521191 | 0.0000000 |
| cg17593958 | cg17593958 | HELZ2 | 0.9401700 | 0.0000000 |
| cg11779113 | cg11779113 | HELZ2 | 0.5030812 | 0.0144080 |
| cg06064964 | cg06064964 | HELZ2 | 0.7573440 | 0.0000286 |
| cg09844573 | cg09844573 | HELZ2 | 0.5751135 | 0.0040931 |
| cg08122652 | cg08122652 | PARP9 | 0.7913177 | 0.0000041 |
| cg00959259 | cg00959259 | PARP9 | 0.6063288 | 0.0016849 |
| cg17326313 | cg17326313 | EIF2AK2 | 0.8385426 | 0.0000003 |
| cg02016764 | cg02016764 | TLR1 | 0.9051719 | 0.0000209 |
| cg01081438 | cg01081438 | BRDT | 0.9295378 | 0.0000000 |
| cg10850215 | cg10850215 | HLA-DPB1 | 0.5787968 | 0.0038085 |
| cg03229061 | cg03229061 | HLA-DPB1 | 0.5742491 | 0.0041624 |
| cg17588455 | cg17588455 | HLA-DPB1 | 0.6503313 | 0.0007807 |
| cg26645432 | cg26645432 | HLA-DPB1 | -0.1544432 | 0.4816708 |
| cg06437840 | cg06437840 | HLA-DPB1 | 0.6946460 | 0.0002351 |
| cg14870156 | cg14870156 | HLA-DPB1 | 0.1173008 | 0.5940133 |
| cg19990651 | cg19990651 | HLA-DPB1 | 0.5971490 | 0.0026261 |
| cg01132696 | cg01132696 | HLA-DPB1 | 0.4154478 | 0.0486716 |
| cg03607951 | cg03607951 | IFI44L | 0.8475412 | 0.0000002 |
| cg17980508 | cg17980508 | IFI44L | 0.8752929 | 0.0000000 |
| cg00855901 | cg00855901 | IFI44L | 0.9405970 | 0.0000000 |
| cg05432003 | cg05432003 | IFITM1 | -0.0256578 | 0.9306198 |
| cg24961286 | cg24961286 | SMAD3 | 0.9522798 | 0.0000000 |
| cg05372444 | cg05372444 | UPK3B | 0.0752061 | 0.7268941 |
| cg16453056 | cg16453056 | UPK3B | -0.0248870 | 0.9081045 |
| cg18719665 | cg18719665 | TTC39C | 0.9106746 | 0.0000000 |
| cg05401069 | cg05401069 | TTC39C | 0.9321970 | 0.0000000 |
| cg12639429 | cg12639429 | TTC39C | 0.9401501 | 0.0000000 |
| cg02891314 | cg02891314 | GFPT2 | 0.9790054 | 0.0000000 |
| cg23248424 | cg23248424 | GFPT2 | 0.9675930 | 0.0000000 |
| cg11738485 | cg11738485 | HOOK2 | 0.9689259 | 0.0000000 |
| cg13944838 | cg13944838 | GFPT2 | 0.9249767 | 0.0000000 |
| cg24345856 | cg24345856 | FAM132A | 0.9804414 | 0.0000000 |
2.2.4 Figure1: The Correlation of all CpGsites between two techniques in CD4+ T cells
[1] "The Correlation r^2 of the two techniques in CD4+ T cells is 0.861615"
2.2.5 Figure2: The Correlation of all CpGsites between two techniques in CD8+ T cells
[1] "The Correlation r^2 of the two techniques in CD8+ T cells is 0.898798"
2.2.6 Figure3: The Correlation of all CpGsites between two techniques in CD4+ and CD8+ T cells
[1] "The Correlation r^2 of the two techniques in CD4+ and CD8+ T cells is 0.879452"
2.2.7 Figure4 : The correlation between the correlation r^2 and coverage depth
2.3 Part I Summary:
In Part I, we conducted several quality control analysis to reveal the quality of NGS sequencing validation data, and compared it with the DNA methylation 450K datasets with the same CpGsites and same samples. And we found that the correlation of the two techniques is relatively good and showed no difference between CD4+ and CD8+ T cells, indicating its unbiased characteristics. Also, we found that the NGS sequencing depth is very high, with mean depth reached nearly 1000x, indicating its robustness for methylation status detection. In conclusion, we found the bisulfite sequencing with high coverage is a robust method for methylation status detection and showed strong linear correlation with the results came from DNA methylation 450K microarry datasets. Thus we can safely use the results of the bisulfite sequencing data for our further analysis.
3 Part II: Validation of differential methylated CpGsites with MethylTarget technology
3.1 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD4+
3.1.1 Validation of differential methylated CpGsites between SSc patients and Controls
3.1.1.1 Table 7: The Differential methylated CpGsites between SSc patients and Controls
| Gene | Pos | Mean.CD4.SSc | Mean.CD4.NC | P.value.CD4.SSC.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 38 | EIF2AK2 | 37383568 | 0.1233814 | 0.1826725 | 0.0000315 | 0.0017293 | cg17326313 |
| 27 | PARP9 | 122281975 | 0.4276390 | 0.5290290 | 0.0000693 | 0.0017293 | cg00959259 |
| 52 | IFI44L | 79085586 | 0.6726998 | 0.7436687 | 0.0000910 | 0.0017293 | cg03607951 |
| 24 | IFITM1 | 313354 | 0.2627358 | 0.3098730 | 0.0011124 | 0.0158510 | cg11694510 |
| 26 | PARP9 | 122281939 | 0.7183252 | 0.7916144 | 0.0015986 | 0.0182241 | cg08122652 |
| 1 | MX1 | 42798747 | 0.0572312 | 0.0650165 | 0.0024990 | 0.0237408 | cg08924203 |
| 34 | HELZ2 | 62199181 | 0.0651395 | 0.0373344 | 0.0055478 | 0.0451752 | cg06064964 |
| 43 | BRDT | 92417998 | 0.4365022 | 0.3211686 | 0.0259938 | 0.1852058 | cg01081438 |
| 54 | IFI44L | 79085765 | 0.4548280 | 0.4984651 | 0.0311206 | 0.1970972 | cg00855901 |
| 42 | FAM132A | 1178246 | 0.7422693 | 0.8213389 | 0.0357950 | 0.1996182 | cg24345856 |
| 30 | BRDT | 92414782 | 0.7324310 | 0.7659456 | 0.0385228 | 0.1996182 | cg02935097 |
| 33 | HELZ2 | 62199156 | 0.0326060 | 0.0191877 | 0.0515001 | 0.2446256 | cg11779113 |
| 32 | HELZ2 | 62199034 | 0.1286726 | 0.0909342 | 0.0741810 | 0.3252549 | cg17593958 |
| 49 | HLA-DPB1 | 33048540 | 0.8897127 | 0.9221222 | 0.0855347 | 0.3482483 | cg14870156 |
| 53 | IFI44L | 79085713 | 0.6427472 | 0.6830388 | 0.1218293 | 0.4629515 | cg17980508 |
| 29 | BRDT | 92414737 | 0.5443314 | 0.5645251 | 0.1433180 | 0.4913739 | cg13299824 |
| 19 | RNF39 | 30039466 | 0.2044569 | 0.2484926 | 0.1550571 | 0.4913739 | cg16078649 |
| 47 | HLA-DPB1 | 33048502 | 0.9067644 | 0.9422507 | 0.1610061 | 0.4913739 | cg26645432 |
| 28 | BRDT | 92414722 | 0.3656732 | 0.3848972 | 0.1637913 | 0.4913739 | cg14732540 |
| 13 | RNF39 | 30039380 | 0.2090533 | 0.2633600 | 0.1855721 | 0.5288806 | cg13918754 |
| 35 | HELZ2 | 62199190 | 0.0445401 | 0.0314240 | 0.2382437 | 0.6214909 | cg09844573 |
| 5 | COX7A2 | 75953853 | 0.2056934 | 0.2195010 | 0.2449027 | 0.6214909 | cg06809298 |
| 31 | COX7A2 | 75954053 | 0.6797633 | 0.7130981 | 0.2507770 | 0.6214909 | cg25716013 |
| 8 | HLA-DPB1 | 33048286 | 0.8099935 | 0.8510260 | 0.2673529 | 0.6349633 | cg09234582 |
| 10 | HLA-DPB1 | 33048310 | 0.8032586 | 0.8410928 | 0.2981181 | 0.6797093 | cg13349035 |
| 55 | IFITM1 | 312518 | 0.0490676 | 0.0631639 | 0.3580291 | 0.7849100 | cg05432003 |
| 48 | HLA-DPB1 | 33048529 | 0.8921467 | 0.9204202 | 0.3763096 | 0.7944315 | cg06437840 |
| 56 | UPK3B | 76145673 | 0.6233565 | 0.6362010 | 0.4024983 | 0.8193716 | cg05372444 |
| 16 | RNF39 | 30039432 | 0.4834165 | 0.5140914 | 0.4185187 | 0.8226057 | cg13401893 |
| 9 | HLA-DPB1 | 33048291 | 0.8495713 | 0.8788058 | 0.4612102 | 0.8661700 | cg25045942 |
| 11 | RNF39 | 30039374 | 0.2369935 | 0.2837008 | 0.4710749 | 0.8661700 | cg20249327 |
| 50 | HLA-DPB1 | 33048555 | 0.8798610 | 0.9063878 | 0.5083086 | 0.8721866 | cg19990651 |
| 4 | RNF39 | 30039175 | 0.2645229 | 0.2484897 | 0.5101264 | 0.8721866 | cg03343571 |
| 15 | RNF39 | 30039408 | 0.2505998 | 0.2834426 | 0.5302796 | 0.8721866 | cg07382347 |
| 36 | GFPT2 | 179741121 | 0.6099365 | 0.5804630 | 0.5355532 | 0.8721866 | cg02891314 |
| 20 | RNF39 | 30039476 | 0.3121350 | 0.3567159 | 0.5829150 | 0.8743192 | cg10930308 |
| 39 | TLR1 | 38805732 | 0.1407696 | 0.1252848 | 0.5838557 | 0.8743192 | cg02016764 |
| 41 | GFPT2 | 179740915 | 0.6507088 | 0.6231930 | 0.6085513 | 0.8743192 | cg13944838 |
| 51 | HLA-DPB1 | 33048558 | 0.8833427 | 0.9128768 | 0.6085841 | 0.8743192 | cg01132696 |
| 37 | GFPT2 | 179741105 | 0.5669895 | 0.5403248 | 0.6135573 | 0.8743192 | cg23248424 |
| 18 | RNF39 | 30039442 | 0.5046425 | 0.5320067 | 0.6554747 | 0.9112697 | cg10568066 |
| 17 | RNF39 | 30039435 | 0.4208703 | 0.4520116 | 0.6785132 | 0.9208393 | cg12633154 |
| 12 | RNF39 | 30039376 | 0.2624746 | 0.2953810 | 0.7094274 | 0.9237632 | cg15877520 |
| 3 | RNF39 | 30039151 | 0.1071649 | 0.1074936 | 0.7130804 | 0.9237632 | cg18930910 |
| 7 | SMAD3 | 67361773 | 0.5495308 | 0.5643506 | 0.7536808 | 0.9278314 | cg24961286 |
| 45 | HLA-DPB1 | 33048483 | 0.8869167 | 0.9152459 | 0.7566380 | 0.9278314 | cg03229061 |
| 6 | COX7A2 | 75953935 | 0.0872796 | 0.0873752 | 0.7650540 | 0.9278314 | cg19367436 |
| 2 | RNF39 | 30039142 | 0.1191231 | 0.1084619 | 0.8291989 | 0.9620290 | cg00947782 |
| 46 | HLA-DPB1 | 33048485 | 0.8542852 | 0.8782200 | 0.8463198 | 0.9620290 | cg17588455 |
| 25 | HOOK2 | 12877188 | 0.3100569 | 0.3262296 | 0.8594934 | 0.9620290 | cg23899408 |
| 21 | TTC39C | 21572657 | 0.1164864 | 0.1077130 | 0.8670164 | 0.9620290 | cg18719665 |
| 57 | UPK3B | 76145633 | 0.6969410 | 0.7009889 | 0.8776405 | 0.9620290 | cg16453056 |
| 40 | HOOK2 | 12877001 | 0.2608195 | 0.2961543 | 0.9123817 | 0.9812407 | cg11738485 |
| 22 | TTC39C | 21572635 | 0.2504695 | 0.2470906 | 0.9656566 | 0.9880360 | cg05401069 |
| 23 | TTC39C | 21572623 | 0.2459859 | 0.2419658 | 0.9656566 | 0.9880360 | cg12639429 |
| 14 | RNF39 | 30039403 | 0.4156483 | 0.4382731 | 0.9804417 | 0.9880360 | cg09279736 |
| 44 | HLA-DPB1 | 33048469 | 0.8456642 | 0.8746810 | 0.9880360 | 0.9880360 | cg10850215 |
3.1.1.2 Figure5: The Differential methylated CpGsites between SSc patients and Controls
[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD4+ T cells is 7"
[1] "Plot the figure of EIF2AK2 cg17326313"
[1] "Plot the figure of PARP9 cg00959259"
[1] "Plot the figure of IFI44L cg03607951"
[1] "Plot the figure of IFITM1 cg11694510"
[1] "Plot the figure of PARP9 cg08122652"
[1] "Plot the figure of MX1 cg08924203"
[1] "Plot the figure of HELZ2 cg06064964"
3.1.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
3.1.2.1 Table 8: The Differential methylated CpGsites between dcSSc patients and Controls
| Gene | Pos | Mean.CD4.dc | Mean.CD4.NC | P.value.CD4.dc.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 5 | COX7A2 | 75953853 | 0.1582780 | 0.2195010 | 0.0029650 | 0.0828283 | cg06809298 |
| 38 | EIF2AK2 | 37383568 | 0.1382443 | 0.1826725 | 0.0065317 | 0.0828283 | cg17326313 |
| 52 | IFI44L | 79085586 | 0.6998180 | 0.7436687 | 0.0067221 | 0.0828283 | cg03607951 |
| 31 | COX7A2 | 75954053 | 0.6191697 | 0.7130981 | 0.0077760 | 0.0828283 | cg25716013 |
| 27 | PARP9 | 122281975 | 0.4618118 | 0.5290290 | 0.0078438 | 0.0828283 | cg00959259 |
| 49 | HLA-DPB1 | 33048540 | 0.8485089 | 0.9221222 | 0.0087188 | 0.0828283 | cg14870156 |
| 50 | HLA-DPB1 | 33048555 | 0.8322881 | 0.9063878 | 0.0202448 | 0.1511792 | cg19990651 |
| 8 | HLA-DPB1 | 33048286 | 0.7585495 | 0.8510260 | 0.0221044 | 0.1511792 | cg09234582 |
| 10 | HLA-DPB1 | 33048310 | 0.7549862 | 0.8410928 | 0.0284030 | 0.1511792 | cg13349035 |
| 47 | HLA-DPB1 | 33048502 | 0.8621385 | 0.9422507 | 0.0290367 | 0.1511792 | cg26645432 |
| 43 | BRDT | 92417998 | 0.4807120 | 0.3211686 | 0.0291749 | 0.1511792 | cg01081438 |
| 6 | COX7A2 | 75953935 | 0.0708456 | 0.0873752 | 0.0320718 | 0.1523412 | cg19367436 |
| 26 | PARP9 | 122281939 | 0.7555214 | 0.7916144 | 0.0393835 | 0.1726815 | cg08122652 |
| 48 | HLA-DPB1 | 33048529 | 0.8453626 | 0.9204202 | 0.0448613 | 0.1826497 | cg06437840 |
| 1 | MX1 | 42798747 | 0.0613389 | 0.0650165 | 0.0625835 | 0.2378174 | cg08924203 |
| 9 | HLA-DPB1 | 33048291 | 0.8106489 | 0.8788058 | 0.0705215 | 0.2512328 | cg25045942 |
| 46 | HLA-DPB1 | 33048485 | 0.8065949 | 0.8782200 | 0.0901437 | 0.2854550 | cg17588455 |
| 51 | HLA-DPB1 | 33048558 | 0.8400719 | 0.9128768 | 0.0901437 | 0.2854550 | cg01132696 |
| 24 | IFITM1 | 313354 | 0.2903140 | 0.3098730 | 0.1562886 | 0.4688659 | cg11694510 |
| 19 | RNF39 | 30039466 | 0.1980040 | 0.2484926 | 0.1673785 | 0.4770286 | cg16078649 |
| 34 | HELZ2 | 62199181 | 0.0485558 | 0.0373344 | 0.1926590 | 0.5135914 | cg06064964 |
| 54 | IFI44L | 79085765 | 0.4823066 | 0.4984651 | 0.2048245 | 0.5135914 | cg00855901 |
| 30 | BRDT | 92414782 | 0.7355643 | 0.7659456 | 0.2133566 | 0.5135914 | cg02935097 |
| 33 | HELZ2 | 62199156 | 0.0271085 | 0.0191877 | 0.2190334 | 0.5135914 | cg11779113 |
| 3 | RNF39 | 30039151 | 0.0913823 | 0.1074936 | 0.2319753 | 0.5135914 | cg18930910 |
| 7 | SMAD3 | 67361773 | 0.6247913 | 0.5643506 | 0.2392935 | 0.5135914 | cg24961286 |
| 2 | RNF39 | 30039142 | 0.1024869 | 0.1084619 | 0.2505736 | 0.5135914 | cg00947782 |
| 56 | UPK3B | 76145673 | 0.6251090 | 0.6362010 | 0.2522905 | 0.5135914 | cg05372444 |
| 4 | RNF39 | 30039175 | 0.2371108 | 0.2484897 | 0.2814859 | 0.5466522 | cg03343571 |
| 45 | HLA-DPB1 | 33048483 | 0.8503734 | 0.9152459 | 0.2877117 | 0.5466522 | cg03229061 |
| 13 | RNF39 | 30039380 | 0.2058499 | 0.2633600 | 0.3159570 | 0.5777219 | cg13918754 |
| 44 | HLA-DPB1 | 33048469 | 0.8001562 | 0.8746810 | 0.3328402 | 0.5777219 | cg10850215 |
| 11 | RNF39 | 30039374 | 0.2305346 | 0.2837008 | 0.3435172 | 0.5777219 | cg20249327 |
| 22 | TTC39C | 21572635 | 0.2332309 | 0.2470906 | 0.3446061 | 0.5777219 | cg05401069 |
| 42 | FAM132A | 1178246 | 0.8489704 | 0.8213389 | 0.3926775 | 0.6208186 | cg24345856 |
| 18 | RNF39 | 30039442 | 0.4861955 | 0.5320067 | 0.3991158 | 0.6208186 | cg10568066 |
| 28 | BRDT | 92414722 | 0.3675997 | 0.3848972 | 0.4029875 | 0.6208186 | cg14732540 |
| 36 | GFPT2 | 179741121 | 0.6390522 | 0.5804630 | 0.4240775 | 0.6361162 | cg02891314 |
| 37 | GFPT2 | 179741105 | 0.5964695 | 0.5403248 | 0.4529365 | 0.6491525 | cg23248424 |
| 23 | TTC39C | 21572623 | 0.2302636 | 0.2419658 | 0.4555456 | 0.6491525 | cg12639429 |
| 17 | RNF39 | 30039435 | 0.4065901 | 0.4520116 | 0.4794792 | 0.6665930 | cg12633154 |
| 20 | RNF39 | 30039476 | 0.3049676 | 0.3567159 | 0.4929225 | 0.6679323 | cg10930308 |
| 15 | RNF39 | 30039408 | 0.2471065 | 0.2834426 | 0.5106213 | 0.6679323 | cg07382347 |
| 21 | TTC39C | 21572657 | 0.1065458 | 0.1077130 | 0.5234849 | 0.6679323 | cg18719665 |
| 41 | GFPT2 | 179740915 | 0.6795025 | 0.6231930 | 0.5352826 | 0.6679323 | cg13944838 |
| 16 | RNF39 | 30039432 | 0.4732537 | 0.5140914 | 0.5469832 | 0.6679323 | cg13401893 |
| 29 | BRDT | 92414737 | 0.5535320 | 0.5645251 | 0.5507512 | 0.6679323 | cg13299824 |
| 53 | IFI44L | 79085713 | 0.6809374 | 0.6830388 | 0.6192145 | 0.7353172 | cg17980508 |
| 12 | RNF39 | 30039376 | 0.2577388 | 0.2953810 | 0.6365307 | 0.7404541 | cg15877520 |
| 14 | RNF39 | 30039403 | 0.3974284 | 0.4382731 | 0.6663552 | 0.7573606 | cg09279736 |
| 55 | IFITM1 | 312518 | 0.0555557 | 0.0631639 | 0.6776384 | 0.7573606 | cg05432003 |
| 35 | HELZ2 | 62199190 | 0.0293048 | 0.0314240 | 0.7006219 | 0.7679894 | cg09844573 |
| 32 | HELZ2 | 62199034 | 0.1061342 | 0.0909342 | 0.7890495 | 0.8387980 | cg17593958 |
| 25 | HOOK2 | 12877188 | 0.3005064 | 0.3262296 | 0.7946507 | 0.8387980 | cg23899408 |
| 40 | HOOK2 | 12877001 | 0.2393487 | 0.2961543 | 0.8224753 | 0.8523835 | cg11738485 |
| 39 | TLR1 | 38805732 | 0.1288417 | 0.1252848 | 0.9908838 | 1.0000000 | cg02016764 |
| 57 | UPK3B | 76145633 | 0.6945542 | 0.7009889 | 1.0000000 | 1.0000000 | cg16453056 |
3.1.2.2 Figure6: The Differential methylated CpGsites between dcSSc patients and Controls
[1] "As there are no CpGsite showed significant difference between dcSSc patients and controls, there is no Figure 6 in our analysis."
3.1.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
3.1.3.1 Table 9: The Differential methylated CpGsites between lcSSc patients and Controls
| Gene | Pos | Mean.CD4.lc | Mean.CD4.NC | P.value.CD4.lc.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 38 | EIF2AK2 | 37383568 | 0.1140921 | 0.1826725 | 0.0001064 | 0.0056791 | cg17326313 |
| 27 | PARP9 | 122281975 | 0.4062810 | 0.5290290 | 0.0002542 | 0.0056791 | cg00959259 |
| 24 | IFITM1 | 313354 | 0.2443503 | 0.3098730 | 0.0002989 | 0.0056791 | cg11694510 |
| 52 | IFI44L | 79085586 | 0.6557509 | 0.7436687 | 0.0004057 | 0.0057818 | cg03607951 |
| 34 | HELZ2 | 62199181 | 0.0761952 | 0.0373344 | 0.0026312 | 0.0285027 | cg06064964 |
| 26 | PARP9 | 122281939 | 0.6950776 | 0.7916144 | 0.0033381 | 0.0285027 | cg08122652 |
| 1 | MX1 | 42798747 | 0.0544927 | 0.0650165 | 0.0035003 | 0.0285027 | cg08924203 |
| 42 | FAM132A | 1178246 | 0.6711351 | 0.8213389 | 0.0176429 | 0.1130039 | cg24345856 |
| 32 | HELZ2 | 62199034 | 0.1436982 | 0.0909342 | 0.0178427 | 0.1130039 | cg17593958 |
| 54 | IFI44L | 79085765 | 0.4376539 | 0.4984651 | 0.0348712 | 0.1987658 | cg00855901 |
| 30 | BRDT | 92414782 | 0.7303421 | 0.7659456 | 0.0431068 | 0.2128604 | cg02935097 |
| 35 | HELZ2 | 62199190 | 0.0546971 | 0.0314240 | 0.0448127 | 0.2128604 | cg09844573 |
| 33 | HELZ2 | 62199156 | 0.0362710 | 0.0191877 | 0.0606307 | 0.2658423 | cg11779113 |
| 53 | IFI44L | 79085713 | 0.6188783 | 0.6830388 | 0.0687262 | 0.2782739 | cg17980508 |
| 4 | RNF39 | 30039175 | 0.2827976 | 0.2484897 | 0.0732300 | 0.2782739 | cg03343571 |
| 29 | BRDT | 92414737 | 0.5381976 | 0.5645251 | 0.0994260 | 0.3542053 | cg13299824 |
| 43 | BRDT | 92417998 | 0.4070290 | 0.3211686 | 0.1260836 | 0.4227508 | cg01081438 |
| 28 | BRDT | 92414722 | 0.3643889 | 0.3848972 | 0.1742262 | 0.5517164 | cg14732540 |
| 45 | HLA-DPB1 | 33048483 | 0.9112788 | 0.9152459 | 0.2034523 | 0.6103568 | cg03229061 |
| 6 | COX7A2 | 75953935 | 0.0987120 | 0.0873752 | 0.2214451 | 0.6311185 | cg19367436 |
| 2 | RNF39 | 30039142 | 0.1302140 | 0.1084619 | 0.2336400 | 0.6341658 | cg00947782 |
| 13 | RNF39 | 30039380 | 0.2111889 | 0.2633600 | 0.2575123 | 0.6671909 | cg13918754 |
| 46 | HLA-DPB1 | 33048485 | 0.8860788 | 0.8782200 | 0.3177340 | 0.7642193 | cg17588455 |
| 19 | RNF39 | 30039466 | 0.2087589 | 0.2484926 | 0.3217765 | 0.7642193 | cg16078649 |
| 55 | IFITM1 | 312518 | 0.0458236 | 0.0631639 | 0.3364106 | 0.7670161 | cg05432003 |
| 39 | TLR1 | 38805732 | 0.1489023 | 0.1252848 | 0.4332000 | 0.9158092 | cg02016764 |
| 50 | HLA-DPB1 | 33048555 | 0.9115762 | 0.9063878 | 0.4338044 | 0.9158092 | cg19990651 |
| 21 | TTC39C | 21572657 | 0.1231134 | 0.1077130 | 0.4609924 | 0.9187244 | cg18719665 |
| 44 | HLA-DPB1 | 33048469 | 0.8760028 | 0.8746810 | 0.4772753 | 0.9187244 | cg10850215 |
| 16 | RNF39 | 30039432 | 0.4901918 | 0.5140914 | 0.4835392 | 0.9187244 | cg13401893 |
| 22 | TTC39C | 21572635 | 0.2619618 | 0.2470906 | 0.5128915 | 0.9294981 | cg05401069 |
| 23 | TTC39C | 21572623 | 0.2564674 | 0.2419658 | 0.5218235 | 0.9294981 | cg12639429 |
| 5 | COX7A2 | 75953853 | 0.2386779 | 0.2195010 | 0.5694953 | 0.9352133 | cg06809298 |
| 51 | HLA-DPB1 | 33048558 | 0.9121899 | 0.9128768 | 0.5905075 | 0.9352133 | cg01132696 |
| 49 | HLA-DPB1 | 33048540 | 0.9171819 | 0.9221222 | 0.6129827 | 0.9352133 | cg14870156 |
| 7 | SMAD3 | 67361773 | 0.4993572 | 0.5643506 | 0.6608297 | 0.9352133 | cg24961286 |
| 15 | RNF39 | 30039408 | 0.2529286 | 0.2834426 | 0.6918790 | 0.9352133 | cg07382347 |
| 3 | RNF39 | 30039151 | 0.1176867 | 0.1074936 | 0.7096815 | 0.9352133 | cg18930910 |
| 47 | HLA-DPB1 | 33048502 | 0.9365151 | 0.9422507 | 0.7145440 | 0.9352133 | cg26645432 |
| 40 | HOOK2 | 12877001 | 0.2751334 | 0.2961543 | 0.7359427 | 0.9352133 | cg11738485 |
| 31 | COX7A2 | 75954053 | 0.7201590 | 0.7130981 | 0.7413143 | 0.9352133 | cg25716013 |
| 56 | UPK3B | 76145673 | 0.6221882 | 0.6362010 | 0.7497569 | 0.9352133 | cg05372444 |
| 11 | RNF39 | 30039374 | 0.2412995 | 0.2837008 | 0.7608970 | 0.9352133 | cg20249327 |
| 9 | HLA-DPB1 | 33048291 | 0.8755195 | 0.8788058 | 0.7626484 | 0.9352133 | cg25045942 |
| 14 | RNF39 | 30039403 | 0.4277949 | 0.4382731 | 0.7716939 | 0.9352133 | cg09279736 |
| 36 | GFPT2 | 179741121 | 0.5905260 | 0.5804630 | 0.7841616 | 0.9352133 | cg02891314 |
| 20 | RNF39 | 30039476 | 0.3169132 | 0.3567159 | 0.7949805 | 0.9352133 | cg10930308 |
| 41 | GFPT2 | 179740915 | 0.6315130 | 0.6231930 | 0.7990228 | 0.9352133 | cg13944838 |
| 48 | HLA-DPB1 | 33048529 | 0.9233361 | 0.9204202 | 0.8115257 | 0.9352133 | cg06437840 |
| 57 | UPK3B | 76145633 | 0.6985323 | 0.7009889 | 0.8203625 | 0.9352133 | cg16453056 |
| 12 | RNF39 | 30039376 | 0.2656319 | 0.2953810 | 0.8651315 | 0.9493894 | cg15877520 |
| 37 | GFPT2 | 179741105 | 0.5473362 | 0.5403248 | 0.8818589 | 0.9493894 | cg23248424 |
| 10 | HLA-DPB1 | 33048310 | 0.8354402 | 0.8410928 | 0.8827656 | 0.9493894 | cg13349035 |
| 8 | HLA-DPB1 | 33048286 | 0.8442894 | 0.8510260 | 0.9049794 | 0.9552561 | cg09234582 |
| 17 | RNF39 | 30039435 | 0.4303904 | 0.4520116 | 0.9607979 | 0.9787582 | cg12633154 |
| 25 | HOOK2 | 12877188 | 0.3164238 | 0.3262296 | 0.9615870 | 0.9787582 | cg23899408 |
| 18 | RNF39 | 30039442 | 0.5169406 | 0.5320067 | 1.0000000 | 1.0000000 | cg10568066 |
3.1.3.2 Figure7: The Differential methylated CpGsites between lcSSc patients and Controls
[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD4+ T cells is 7"
[1] "Plot the figure of EIF2AK2 cg17326313"
[1] "Plot the figure of PARP9 cg00959259"
[1] "Plot the figure of IFITM1 cg11694510"
[1] "Plot the figure of IFI44L cg03607951"
[1] "Plot the figure of HELZ2 cg06064964"
[1] "Plot the figure of PARP9 cg08122652"
[1] "Plot the figure of MX1 cg08924203"
3.1.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
3.1.4.1 Table 10: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
| Gene | Pos | Mean.CD4.dc | Mean.CD4.lc | P.value.CD4.dc.lc | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 5 | COX7A2 | 75953853 | 0.1582780 | 0.2386779 | 0.0071676 | 0.2096029 | cg06809298 |
| 50 | HLA-DPB1 | 33048555 | 0.8322881 | 0.9115762 | 0.0122522 | 0.2096029 | cg19990651 |
| 31 | COX7A2 | 75954053 | 0.6191697 | 0.7201590 | 0.0156750 | 0.2096029 | cg25716013 |
| 6 | COX7A2 | 75953935 | 0.0708456 | 0.0987120 | 0.0172076 | 0.2096029 | cg19367436 |
| 24 | IFITM1 | 313354 | 0.2903140 | 0.2443503 | 0.0183862 | 0.2096029 | cg11694510 |
| 46 | HLA-DPB1 | 33048485 | 0.8065949 | 0.8860788 | 0.0312288 | 0.2812870 | cg17588455 |
| 4 | RNF39 | 30039175 | 0.2371108 | 0.2827976 | 0.0386756 | 0.2812870 | cg03343571 |
| 8 | HLA-DPB1 | 33048286 | 0.7585495 | 0.8442894 | 0.0444137 | 0.2812870 | cg09234582 |
| 49 | HLA-DPB1 | 33048540 | 0.8485089 | 0.9171819 | 0.0444137 | 0.2812870 | cg14870156 |
| 48 | HLA-DPB1 | 33048529 | 0.8453626 | 0.9233361 | 0.0604479 | 0.2891391 | cg06437840 |
| 10 | HLA-DPB1 | 33048310 | 0.7549862 | 0.8354402 | 0.0618647 | 0.2891391 | cg13349035 |
| 47 | HLA-DPB1 | 33048502 | 0.8621385 | 0.9365151 | 0.0659440 | 0.2891391 | cg26645432 |
| 51 | HLA-DPB1 | 33048558 | 0.8400719 | 0.9121899 | 0.0659440 | 0.2891391 | cg01132696 |
| 35 | HELZ2 | 62199190 | 0.0293048 | 0.0546971 | 0.0766858 | 0.3122209 | cg09844573 |
| 2 | RNF39 | 30039142 | 0.1024869 | 0.1302140 | 0.0844665 | 0.3195026 | cg00947782 |
| 9 | HLA-DPB1 | 33048291 | 0.8106489 | 0.8755195 | 0.0896849 | 0.3195026 | cg25045942 |
| 42 | FAM132A | 1178246 | 0.8489704 | 0.6711351 | 0.1264878 | 0.4241061 | cg24345856 |
| 38 | EIF2AK2 | 37383568 | 0.1382443 | 0.1140921 | 0.1464178 | 0.4532251 | cg17326313 |
| 3 | RNF39 | 30039151 | 0.0913823 | 0.1176867 | 0.1510750 | 0.4532251 | cg18930910 |
| 32 | HELZ2 | 62199034 | 0.1061342 | 0.1436982 | 0.1643902 | 0.4685121 | cg17593958 |
| 45 | HLA-DPB1 | 33048483 | 0.8503734 | 0.9112788 | 0.1827480 | 0.4960304 | cg03229061 |
| 7 | SMAD3 | 67361773 | 0.6247913 | 0.4993572 | 0.2220643 | 0.5508070 | cg24961286 |
| 53 | IFI44L | 79085713 | 0.6809374 | 0.6188783 | 0.2228357 | 0.5508070 | cg17980508 |
| 34 | HELZ2 | 62199181 | 0.0485558 | 0.0761952 | 0.2319187 | 0.5508070 | cg06064964 |
| 52 | IFI44L | 79085586 | 0.6998180 | 0.6557509 | 0.2456493 | 0.5594492 | cg03607951 |
| 43 | BRDT | 92417998 | 0.4807120 | 0.4070290 | 0.2551874 | 0.5594492 | cg01081438 |
| 22 | TTC39C | 21572635 | 0.2332309 | 0.2619618 | 0.2790440 | 0.5858389 | cg05401069 |
| 44 | HLA-DPB1 | 33048469 | 0.8001562 | 0.8760028 | 0.2877805 | 0.5858389 | cg10850215 |
| 27 | PARP9 | 122281975 | 0.4618118 | 0.4062810 | 0.3234273 | 0.6204948 | cg00959259 |
| 54 | IFI44L | 79085765 | 0.4823066 | 0.4376539 | 0.3377640 | 0.6204948 | cg00855901 |
| 18 | RNF39 | 30039442 | 0.4861955 | 0.5169406 | 0.3408351 | 0.6204948 | cg10568066 |
| 1 | MX1 | 42798747 | 0.0613389 | 0.0544927 | 0.3592338 | 0.6204948 | cg08924203 |
| 23 | TTC39C | 21572623 | 0.2302636 | 0.2564674 | 0.3592338 | 0.6204948 | cg12639429 |
| 26 | PARP9 | 122281939 | 0.7555214 | 0.6950776 | 0.3831148 | 0.6398978 | cg08122652 |
| 14 | RNF39 | 30039403 | 0.3974284 | 0.4277949 | 0.3997432 | 0.6398978 | cg09279736 |
| 21 | TTC39C | 21572657 | 0.1065458 | 0.1231134 | 0.4041460 | 0.6398978 | cg18719665 |
| 29 | BRDT | 92414737 | 0.5535320 | 0.5381976 | 0.4198151 | 0.6467422 | cg13299824 |
| 20 | RNF39 | 30039476 | 0.3049676 | 0.3169132 | 0.4900499 | 0.7350749 | cg10930308 |
| 40 | HOOK2 | 12877001 | 0.2393487 | 0.2751334 | 0.5208424 | 0.7612312 | cg11738485 |
| 36 | GFPT2 | 179741121 | 0.6390522 | 0.5905260 | 0.5570375 | 0.7629681 | cg02891314 |
| 11 | RNF39 | 30039374 | 0.2305346 | 0.2412995 | 0.5714019 | 0.7629681 | cg20249327 |
| 17 | RNF39 | 30039435 | 0.4065901 | 0.4303904 | 0.5755724 | 0.7629681 | cg12633154 |
| 30 | BRDT | 92414782 | 0.7355643 | 0.7303421 | 0.5755724 | 0.7629681 | cg02935097 |
| 37 | GFPT2 | 179741105 | 0.5964695 | 0.5473362 | 0.6328136 | 0.7901433 | cg23248424 |
| 33 | HELZ2 | 62199156 | 0.0271085 | 0.0362710 | 0.6370923 | 0.7901433 | cg11779113 |
| 55 | IFITM1 | 312518 | 0.0555557 | 0.0458236 | 0.6376595 | 0.7901433 | cg05432003 |
| 39 | TLR1 | 38805732 | 0.1288417 | 0.1489023 | 0.6648621 | 0.7982768 | cg02016764 |
| 15 | RNF39 | 30039408 | 0.2471065 | 0.2529286 | 0.6722331 | 0.7982768 | cg07382347 |
| 19 | RNF39 | 30039466 | 0.1980040 | 0.2087589 | 0.7093540 | 0.8123098 | cg16078649 |
| 41 | GFPT2 | 179740915 | 0.6795025 | 0.6315130 | 0.7125525 | 0.8123098 | cg13944838 |
| 12 | RNF39 | 30039376 | 0.2577388 | 0.2656319 | 0.7536718 | 0.8329511 | cg15877520 |
| 16 | RNF39 | 30039432 | 0.4732537 | 0.4901918 | 0.7718955 | 0.8329511 | cg13401893 |
| 13 | RNF39 | 30039380 | 0.2058499 | 0.2111889 | 0.7744984 | 0.8329511 | cg13918754 |
| 28 | BRDT | 92414722 | 0.3675997 | 0.3643889 | 0.8166164 | 0.8619840 | cg14732540 |
| 25 | HOOK2 | 12877188 | 0.3005064 | 0.3164238 | 0.8807380 | 0.9127649 | cg23899408 |
| 56 | UPK3B | 76145673 | 0.6251090 | 0.6221882 | 0.9011242 | 0.9172157 | cg05372444 |
| 57 | UPK3B | 76145633 | 0.6945542 | 0.6985323 | 0.9891186 | 0.9891186 | cg16453056 |
3.1.4.2 Figure8: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 8 in our analysis."
3.2 Validation of differential methylated CpGsites both in the discovery stage and validation stage in CD8+
3.2.1 Validation of differential methylated CpGsites between SSc patients and Controls
3.2.1.1 Table 11: The Differential methylated CpGsites between SSc patients and Controls
| Gene | Pos | Mean.CD8.SSc | Mean.CD8.NC | P.value.CD8.SSC.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 27 | PARP9 | 122281975 | 0.4531487 | 0.5968228 | 0.0000000 | 0.0000002 | cg00959259 |
| 26 | PARP9 | 122281939 | 0.7320359 | 0.8323341 | 0.0000001 | 0.0000020 | cg08122652 |
| 38 | EIF2AK2 | 37383568 | 0.1373269 | 0.1882193 | 0.0000971 | 0.0018443 | cg17326313 |
| 34 | HELZ2 | 62199181 | 0.0451481 | 0.0214664 | 0.0002035 | 0.0028996 | cg06064964 |
| 21 | TTC39C | 21572657 | 0.1848003 | 0.1419552 | 0.0003293 | 0.0037542 | cg18719665 |
| 54 | IFI44L | 79085765 | 0.5151405 | 0.6067145 | 0.0011990 | 0.0113905 | cg00855901 |
| 22 | TTC39C | 21572635 | 0.3820672 | 0.3329965 | 0.0054331 | 0.0442407 | cg05401069 |
| 32 | HELZ2 | 62199034 | 0.1427749 | 0.0981128 | 0.0069887 | 0.0451370 | cg17593958 |
| 33 | HELZ2 | 62199156 | 0.0221550 | 0.0106671 | 0.0071269 | 0.0451370 | cg11779113 |
| 35 | HELZ2 | 62199190 | 0.0334972 | 0.0185647 | 0.0096154 | 0.0545651 | cg09844573 |
| 23 | TTC39C | 21572623 | 0.3587072 | 0.3148537 | 0.0105301 | 0.0545651 | cg12639429 |
| 53 | IFI44L | 79085713 | 0.6866851 | 0.7410939 | 0.0116753 | 0.0554579 | cg17980508 |
| 20 | RNF39 | 30039476 | 0.3051805 | 0.3870814 | 0.0160688 | 0.0704556 | cg10930308 |
| 52 | IFI44L | 79085586 | 0.7097750 | 0.7625005 | 0.0178789 | 0.0727926 | cg03607951 |
| 14 | RNF39 | 30039403 | 0.4364698 | 0.5066883 | 0.0214113 | 0.0810791 | cg09279736 |
| 11 | RNF39 | 30039374 | 0.2453951 | 0.3210745 | 0.0227590 | 0.0810791 | cg20249327 |
| 19 | RNF39 | 30039466 | 0.2398981 | 0.3018692 | 0.0269289 | 0.0902911 | cg16078649 |
| 17 | RNF39 | 30039435 | 0.4457716 | 0.5147477 | 0.0368050 | 0.1165493 | cg12633154 |
| 16 | RNF39 | 30039432 | 0.4890092 | 0.5487349 | 0.0445974 | 0.1337921 | cg13401893 |
| 12 | RNF39 | 30039376 | 0.2472879 | 0.3088533 | 0.0508454 | 0.1410246 | cg15877520 |
| 15 | RNF39 | 30039408 | 0.2767715 | 0.3401470 | 0.0519564 | 0.1410246 | cg07382347 |
| 49 | HLA-DPB1 | 33048540 | 0.8985396 | 0.9300191 | 0.0613516 | 0.1589565 | cg14870156 |
| 18 | RNF39 | 30039442 | 0.5566290 | 0.6089304 | 0.0861232 | 0.2109022 | cg10568066 |
| 51 | HLA-DPB1 | 33048558 | 0.8842849 | 0.9185070 | 0.0915257 | 0.2109022 | cg01132696 |
| 45 | HLA-DPB1 | 33048483 | 0.9146446 | 0.9459825 | 0.0925010 | 0.2109022 | cg03229061 |
| 1 | MX1 | 42798747 | 0.0694463 | 0.0772312 | 0.1102259 | 0.2416490 | cg08924203 |
| 42 | FAM132A | 1178246 | 0.7041153 | 0.7990064 | 0.1274810 | 0.2656621 | cg24345856 |
| 13 | RNF39 | 30039380 | 0.2259111 | 0.2931618 | 0.1305007 | 0.2656621 | cg13918754 |
| 8 | HLA-DPB1 | 33048286 | 0.8528574 | 0.8854463 | 0.1394408 | 0.2735732 | cg09234582 |
| 24 | IFITM1 | 313354 | 0.2657604 | 0.2781218 | 0.1439859 | 0.2735732 | cg11694510 |
| 47 | HLA-DPB1 | 33048502 | 0.9263918 | 0.9495350 | 0.1624473 | 0.2986934 | cg26645432 |
| 10 | HLA-DPB1 | 33048310 | 0.8406343 | 0.8746341 | 0.1713249 | 0.3051725 | cg13349035 |
| 9 | HLA-DPB1 | 33048291 | 0.8783046 | 0.9075440 | 0.1830702 | 0.3162122 | cg25045942 |
| 43 | BRDT | 92417998 | 0.4293984 | 0.3385588 | 0.2222715 | 0.3726315 | cg01081438 |
| 46 | HLA-DPB1 | 33048485 | 0.8838146 | 0.9019680 | 0.2389443 | 0.3891379 | cg17588455 |
| 39 | TLR1 | 38805732 | 0.2242038 | 0.1519158 | 0.2815084 | 0.4457217 | cg02016764 |
| 50 | HLA-DPB1 | 33048555 | 0.9042304 | 0.9244570 | 0.4691117 | 0.7065182 | cg19990651 |
| 41 | GFPT2 | 179740915 | 0.6326464 | 0.6066592 | 0.4710121 | 0.7065182 | cg13944838 |
| 37 | GFPT2 | 179741105 | 0.5720316 | 0.5438813 | 0.5151081 | 0.7458898 | cg23248424 |
| 55 | IFITM1 | 312518 | 0.0591742 | 0.0645218 | 0.5326765 | 0.7458898 | cg05432003 |
| 31 | COX7A2 | 75954053 | 0.6679577 | 0.6796820 | 0.5392675 | 0.7458898 | cg25716013 |
| 36 | GFPT2 | 179741121 | 0.6222384 | 0.5961929 | 0.5496030 | 0.7458898 | cg02891314 |
| 40 | HOOK2 | 12877001 | 0.2531282 | 0.2778928 | 0.6561935 | 0.8698379 | cg11738485 |
| 48 | HLA-DPB1 | 33048529 | 0.8988812 | 0.9228805 | 0.6946645 | 0.8845146 | cg06437840 |
| 6 | COX7A2 | 75953935 | 0.1161680 | 0.1196888 | 0.6983010 | 0.8845146 | cg19367436 |
| 4 | RNF39 | 30039175 | 0.3684328 | 0.3765410 | 0.7489301 | 0.9244078 | cg03343571 |
| 30 | BRDT | 92414782 | 0.5152659 | 0.5015247 | 0.7843399 | 0.9244078 | cg02935097 |
| 5 | COX7A2 | 75953853 | 0.2208525 | 0.2254708 | 0.8146425 | 0.9244078 | cg06809298 |
| 44 | HLA-DPB1 | 33048469 | 0.8432144 | 0.8622766 | 0.8185363 | 0.9244078 | cg10850215 |
| 7 | SMAD3 | 67361773 | 0.5528822 | 0.5717843 | 0.8556844 | 0.9244078 | cg24961286 |
| 3 | RNF39 | 30039151 | 0.1535606 | 0.1491135 | 0.8600892 | 0.9244078 | cg18930910 |
| 56 | UPK3B | 76145673 | 0.6460271 | 0.6409087 | 0.8600892 | 0.9244078 | cg05372444 |
| 2 | RNF39 | 30039142 | 0.1907816 | 0.1891776 | 0.8820034 | 0.9244078 | cg00947782 |
| 57 | UPK3B | 76145633 | 0.6982444 | 0.6990565 | 0.9076810 | 0.9244078 | cg16453056 |
| 28 | BRDT | 92414722 | 0.3303334 | 0.3304857 | 0.9076835 | 0.9244078 | cg14732540 |
| 29 | BRDT | 92414737 | 0.4273772 | 0.4210830 | 0.9081902 | 0.9244078 | cg13299824 |
| 25 | HOOK2 | 12877188 | 0.3265455 | 0.3373459 | 0.9716002 | 0.9716002 | cg23899408 |
3.2.1.2 Figure9 : The Differential methylated CpGsites between SSc patients and Controls
[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD8+ T cells is 9"
[1] "Plot the figure of PARP9 cg00959259"
[1] "Plot the figure of PARP9 cg08122652"
[1] "Plot the figure of EIF2AK2 cg17326313"
[1] "Plot the figure of HELZ2 cg06064964"
[1] "Plot the figure of TTC39C cg18719665"
[1] "Plot the figure of IFI44L cg00855901"
[1] "Plot the figure of TTC39C cg05401069"
[1] "Plot the figure of HELZ2 cg17593958"
[1] "Plot the figure of HELZ2 cg11779113"
3.2.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
3.2.2.1 Table 12: The Differential methylated CpGsites between dcSSc patients and Controls
| Gene | Pos | Mean.CD8.dc | Mean.CD8.NC | P.value.CD8.dc.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 27 | PARP9 | 122281975 | 0.5038614 | 0.5968228 | 0.0000795 | 0.0045336 | cg00959259 |
| 26 | PARP9 | 122281939 | 0.7752162 | 0.8323341 | 0.0004673 | 0.0133193 | cg08122652 |
| 34 | HELZ2 | 62199181 | 0.0403199 | 0.0214664 | 0.0017552 | 0.0333493 | cg06064964 |
| 21 | TTC39C | 21572657 | 0.1751158 | 0.1419552 | 0.0051675 | 0.0736364 | cg18719665 |
| 22 | TTC39C | 21572635 | 0.3737943 | 0.3329965 | 0.0200640 | 0.1460961 | cg05401069 |
| 9 | HLA-DPB1 | 33048291 | 0.8440094 | 0.9075440 | 0.0203633 | 0.1460961 | cg25045942 |
| 10 | HLA-DPB1 | 33048310 | 0.8029228 | 0.8746341 | 0.0203633 | 0.1460961 | cg13349035 |
| 38 | EIF2AK2 | 37383568 | 0.1523055 | 0.1882193 | 0.0205047 | 0.1460961 | cg17326313 |
| 8 | HLA-DPB1 | 33048286 | 0.8158911 | 0.8854463 | 0.0328369 | 0.2079672 | cg09234582 |
| 50 | HLA-DPB1 | 33048555 | 0.8772847 | 0.9244570 | 0.0460668 | 0.2625807 | cg19990651 |
| 23 | TTC39C | 21572623 | 0.3483870 | 0.3148537 | 0.0508476 | 0.2634830 | cg12639429 |
| 51 | HLA-DPB1 | 33048558 | 0.8637292 | 0.9185070 | 0.0602995 | 0.2864225 | cg01132696 |
| 31 | COX7A2 | 75954053 | 0.6152673 | 0.6796820 | 0.0738199 | 0.3236717 | cg25716013 |
| 20 | RNF39 | 30039476 | 0.3027517 | 0.3870814 | 0.0800138 | 0.3257705 | cg10930308 |
| 47 | HLA-DPB1 | 33048502 | 0.9052612 | 0.9495350 | 0.0933254 | 0.3384623 | cg26645432 |
| 6 | COX7A2 | 75953935 | 0.0983593 | 0.1196888 | 0.0985566 | 0.3384623 | cg19367436 |
| 54 | IFI44L | 79085765 | 0.5381196 | 0.6067145 | 0.1010910 | 0.3384623 | cg00855901 |
| 5 | COX7A2 | 75953853 | 0.1791361 | 0.2254708 | 0.1152786 | 0.3384623 | cg06809298 |
| 12 | RNF39 | 30039376 | 0.2454873 | 0.3088533 | 0.1166722 | 0.3384623 | cg15877520 |
| 33 | HELZ2 | 62199156 | 0.0183079 | 0.0106671 | 0.1187587 | 0.3384623 | cg11779113 |
| 49 | HLA-DPB1 | 33048540 | 0.8913260 | 0.9300191 | 0.1367150 | 0.3710835 | cg14870156 |
| 14 | RNF39 | 30039403 | 0.4428490 | 0.5066883 | 0.1455487 | 0.3722053 | cg09279736 |
| 11 | RNF39 | 30039374 | 0.2511929 | 0.3210745 | 0.1613889 | 0.3722053 | cg20249327 |
| 7 | SMAD3 | 67361773 | 0.6526138 | 0.5717843 | 0.1662787 | 0.3722053 | cg24961286 |
| 32 | HELZ2 | 62199034 | 0.1303204 | 0.0981128 | 0.1700332 | 0.3722053 | cg17593958 |
| 36 | GFPT2 | 179741121 | 0.6758027 | 0.5961929 | 0.1766241 | 0.3722053 | cg02891314 |
| 17 | RNF39 | 30039435 | 0.4492864 | 0.5147477 | 0.1784679 | 0.3722053 | cg12633154 |
| 18 | RNF39 | 30039442 | 0.5503101 | 0.6089304 | 0.1844433 | 0.3722053 | cg10568066 |
| 35 | HELZ2 | 62199190 | 0.0282865 | 0.0185647 | 0.1893676 | 0.3722053 | cg09844573 |
| 37 | GFPT2 | 179741105 | 0.6153956 | 0.5438813 | 0.2097935 | 0.3986077 | cg23248424 |
| 41 | GFPT2 | 179740915 | 0.6764403 | 0.6066592 | 0.2263120 | 0.4161220 | cg13944838 |
| 19 | RNF39 | 30039466 | 0.2486829 | 0.3018692 | 0.2494308 | 0.4442987 | cg16078649 |
| 16 | RNF39 | 30039432 | 0.5015302 | 0.5487349 | 0.2969993 | 0.5129987 | cg13401893 |
| 46 | HLA-DPB1 | 33048485 | 0.8731776 | 0.9019680 | 0.3109870 | 0.5213605 | cg17588455 |
| 15 | RNF39 | 30039408 | 0.2907931 | 0.3401470 | 0.3229185 | 0.5254711 | cg07382347 |
| 56 | UPK3B | 76145673 | 0.6591430 | 0.6409087 | 0.3318765 | 0.5254711 | cg05372444 |
| 52 | IFI44L | 79085586 | 0.7342337 | 0.7625005 | 0.3439880 | 0.5293755 | cg03607951 |
| 13 | RNF39 | 30039380 | 0.2266518 | 0.2931618 | 0.3597039 | 0.5293755 | cg13918754 |
| 39 | TLR1 | 38805732 | 0.2455374 | 0.1519158 | 0.3622043 | 0.5293755 | cg02016764 |
| 45 | HLA-DPB1 | 33048483 | 0.9137198 | 0.9459825 | 0.4044165 | 0.5705369 | cg03229061 |
| 53 | IFI44L | 79085713 | 0.7196792 | 0.7410939 | 0.4103862 | 0.5705369 | cg17980508 |
| 43 | BRDT | 92417998 | 0.4218728 | 0.3385588 | 0.5459604 | 0.7409462 | cg01081438 |
| 57 | UPK3B | 76145633 | 0.6889555 | 0.6990565 | 0.5677746 | 0.7526314 | cg16453056 |
| 42 | FAM132A | 1178246 | 0.7904919 | 0.7990064 | 0.5837457 | 0.7551444 | cg24345856 |
| 2 | RNF39 | 30039142 | 0.1778969 | 0.1891776 | 0.5961666 | 0.7551444 | cg00947782 |
| 48 | HLA-DPB1 | 33048529 | 0.8844981 | 0.9228805 | 0.6348471 | 0.7866584 | cg06437840 |
| 3 | RNF39 | 30039151 | 0.1489598 | 0.1491135 | 0.7786131 | 0.9116599 | cg18930910 |
| 55 | IFITM1 | 312518 | 0.0638008 | 0.0645218 | 0.7807075 | 0.9116599 | cg05432003 |
| 28 | BRDT | 92414722 | 0.3375056 | 0.3304857 | 0.7925551 | 0.9116599 | cg14732540 |
| 25 | HOOK2 | 12877188 | 0.3175145 | 0.3373459 | 0.7997017 | 0.9116599 | cg23899408 |
| 44 | HLA-DPB1 | 33048469 | 0.8301764 | 0.8622766 | 0.8163607 | 0.9124032 | cg10850215 |
| 4 | RNF39 | 30039175 | 0.3676492 | 0.3765410 | 0.8347777 | 0.9150448 | cg03343571 |
| 30 | BRDT | 92414782 | 0.5136856 | 0.5015247 | 0.8646147 | 0.9219336 | cg02935097 |
| 29 | BRDT | 92414737 | 0.4350134 | 0.4210830 | 0.8787515 | 0.9219336 | cg13299824 |
| 1 | MX1 | 42798747 | 0.0767360 | 0.0772312 | 0.8951382 | 0.9219336 | cg08924203 |
| 40 | HOOK2 | 12877001 | 0.2404004 | 0.2778928 | 0.9057593 | 0.9219336 | cg11738485 |
| 24 | IFITM1 | 313354 | 0.2827623 | 0.2781218 | 0.9785245 | 0.9785245 | cg11694510 |
3.2.2.2 Figure10 : The Differential methylated CpGsites between dcSSc patients and Controls
[1] "The number of significant differential methylated CpGsites between dcSSc patients and normal controls in CD8+ T cells is 3"
[1] "Plot the figure of PARP9 cg00959259"
[1] "Plot the figure of PARP9 cg08122652"
[1] "Plot the figure of HELZ2 cg06064964"
3.2.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
3.2.3.1 Table 13: The Differential methylated CpGsites between lcSSc patients and Controls
| Gene | Pos | Mean.CD8.lc | Mean.CD8.NC | P.value.CD8.lc.NC | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 27 | PARP9 | 122281975 | 0.4227211 | 0.5968228 | 0.0000000 | 0.0000023 | cg00959259 |
| 26 | PARP9 | 122281939 | 0.7061277 | 0.8323341 | 0.0000004 | 0.0000123 | cg08122652 |
| 38 | EIF2AK2 | 37383568 | 0.1283398 | 0.1882193 | 0.0001445 | 0.0027447 | cg17326313 |
| 54 | IFI44L | 79085765 | 0.5013530 | 0.6067145 | 0.0007354 | 0.0104792 | cg00855901 |
| 21 | TTC39C | 21572657 | 0.1911325 | 0.1419552 | 0.0023798 | 0.0249457 | cg18719665 |
| 34 | HELZ2 | 62199181 | 0.0482206 | 0.0214664 | 0.0030540 | 0.0249457 | cg06064964 |
| 53 | IFI44L | 79085713 | 0.6668886 | 0.7410939 | 0.0030635 | 0.0249457 | cg17980508 |
| 32 | HELZ2 | 62199034 | 0.1507004 | 0.0981128 | 0.0049158 | 0.0350251 | cg17593958 |
| 35 | HELZ2 | 62199190 | 0.0368130 | 0.0185647 | 0.0067862 | 0.0424276 | cg09844573 |
| 33 | HELZ2 | 62199156 | 0.0246032 | 0.0106671 | 0.0074434 | 0.0424276 | cg11779113 |
| 52 | IFI44L | 79085586 | 0.6950998 | 0.7625005 | 0.0082411 | 0.0427037 | cg03607951 |
| 1 | MX1 | 42798747 | 0.0649603 | 0.0772312 | 0.0174810 | 0.0830349 | cg08924203 |
| 19 | RNF39 | 30039466 | 0.2344922 | 0.3018692 | 0.0220196 | 0.0955158 | cg16078649 |
| 22 | TTC39C | 21572635 | 0.3874764 | 0.3329965 | 0.0257309 | 0.0955158 | cg05401069 |
| 11 | RNF39 | 30039374 | 0.2418272 | 0.3210745 | 0.0281741 | 0.0955158 | cg20249327 |
| 14 | RNF39 | 30039403 | 0.4325441 | 0.5066883 | 0.0284098 | 0.0955158 | cg09279736 |
| 23 | TTC39C | 21572623 | 0.3654550 | 0.3148537 | 0.0284872 | 0.0955158 | cg12639429 |
| 20 | RNF39 | 30039476 | 0.3066752 | 0.3870814 | 0.0329618 | 0.1043789 | cg10930308 |
| 24 | IFITM1 | 313354 | 0.2552977 | 0.2781218 | 0.0363332 | 0.1069390 | cg11694510 |
| 16 | RNF39 | 30039432 | 0.4813039 | 0.5487349 | 0.0375225 | 0.1069390 | cg13401893 |
| 15 | RNF39 | 30039408 | 0.2681428 | 0.3401470 | 0.0426072 | 0.1156480 | cg07382347 |
| 17 | RNF39 | 30039435 | 0.4436087 | 0.5147477 | 0.0492870 | 0.1276981 | cg12633154 |
| 42 | FAM132A | 1178246 | 0.6509604 | 0.7990064 | 0.0797333 | 0.1922498 | cg24345856 |
| 45 | HLA-DPB1 | 33048483 | 0.9151426 | 0.9459825 | 0.0809473 | 0.1922498 | cg03229061 |
| 12 | RNF39 | 30039376 | 0.2483960 | 0.3088533 | 0.1050740 | 0.2395688 | cg15877520 |
| 49 | HLA-DPB1 | 33048540 | 0.9024238 | 0.9300191 | 0.1162624 | 0.2548830 | cg14870156 |
| 13 | RNF39 | 30039380 | 0.2254552 | 0.2931618 | 0.1416151 | 0.2955955 | cg13918754 |
| 18 | RNF39 | 30039442 | 0.5605175 | 0.6089304 | 0.1452048 | 0.2955955 | cg10568066 |
| 43 | BRDT | 92417998 | 0.4340296 | 0.3385588 | 0.2019771 | 0.3969894 | cg01081438 |
| 51 | HLA-DPB1 | 33048558 | 0.8953533 | 0.9185070 | 0.2886716 | 0.5484760 | cg01132696 |
| 46 | HLA-DPB1 | 33048485 | 0.8895422 | 0.9019680 | 0.3495811 | 0.6427782 | cg17588455 |
| 47 | HLA-DPB1 | 33048502 | 0.9377699 | 0.9495350 | 0.4261264 | 0.7287358 | cg26645432 |
| 5 | COX7A2 | 75953853 | 0.2458823 | 0.2254708 | 0.4329821 | 0.7287358 | cg06809298 |
| 39 | TLR1 | 38805732 | 0.1967748 | 0.1519158 | 0.4346845 | 0.7287358 | cg02016764 |
| 55 | IFITM1 | 312518 | 0.0545476 | 0.0645218 | 0.4846278 | 0.7892510 | cg05432003 |
| 7 | SMAD3 | 67361773 | 0.4988609 | 0.5717843 | 0.5013891 | 0.7938662 | cg24961286 |
| 6 | COX7A2 | 75953935 | 0.1268532 | 0.1196888 | 0.5333464 | 0.8216418 | cg19367436 |
| 8 | HLA-DPB1 | 33048286 | 0.8756058 | 0.8854463 | 0.5869590 | 0.8578632 | cg09234582 |
| 40 | HOOK2 | 12877001 | 0.2614503 | 0.2778928 | 0.5869590 | 0.8578632 | cg11738485 |
| 44 | HLA-DPB1 | 33048469 | 0.8502348 | 0.8622766 | 0.6349855 | 0.9048543 | cg10850215 |
| 56 | UPK3B | 76145673 | 0.6379558 | 0.6409087 | 0.6554565 | 0.9112444 | cg05372444 |
| 31 | COX7A2 | 75954053 | 0.7003826 | 0.6796820 | 0.6814189 | 0.9247828 | cg25716013 |
| 50 | HLA-DPB1 | 33048555 | 0.9187396 | 0.9244570 | 0.7481197 | 0.9687679 | cg19990651 |
| 4 | RNF39 | 30039175 | 0.3689150 | 0.3765410 | 0.7693881 | 0.9687679 | cg03343571 |
| 10 | HLA-DPB1 | 33048310 | 0.8638414 | 0.8746341 | 0.7934026 | 0.9687679 | cg13349035 |
| 30 | BRDT | 92414782 | 0.5162384 | 0.5015247 | 0.7980256 | 0.9687679 | cg02935097 |
| 57 | UPK3B | 76145633 | 0.7039606 | 0.6990565 | 0.8081719 | 0.9687679 | cg16453056 |
| 48 | HLA-DPB1 | 33048529 | 0.9066260 | 0.9228805 | 0.8286788 | 0.9687679 | cg06437840 |
| 9 | HLA-DPB1 | 33048291 | 0.8994094 | 0.9075440 | 0.8330581 | 0.9687679 | cg25045942 |
| 2 | RNF39 | 30039142 | 0.1987107 | 0.1891776 | 0.8645366 | 0.9687679 | cg00947782 |
| 25 | HOOK2 | 12877188 | 0.3324504 | 0.3373459 | 0.8933038 | 0.9687679 | cg23899408 |
| 41 | GFPT2 | 179740915 | 0.6056963 | 0.6066592 | 0.8933038 | 0.9687679 | cg13944838 |
| 36 | GFPT2 | 179741121 | 0.5892757 | 0.5961929 | 0.9007842 | 0.9687679 | cg02891314 |
| 29 | BRDT | 92414737 | 0.4226780 | 0.4210830 | 0.9636324 | 0.9948029 | cg13299824 |
| 3 | RNF39 | 30039151 | 0.1563919 | 0.1491135 | 0.9685953 | 0.9948029 | cg18930910 |
| 28 | BRDT | 92414722 | 0.3259197 | 0.3304857 | 0.9842946 | 0.9948029 | cg14732540 |
| 37 | GFPT2 | 179741105 | 0.5453461 | 0.5438813 | 0.9948029 | 0.9948029 | cg23248424 |
3.2.3.2 Figure11: The Differential methylated CpGsites between lcSSc patients and Controls
[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD8+ T cells is 11"
[1] "Plot the figure of PARP9 cg00959259"
[1] "Plot the figure of PARP9 cg08122652"
[1] "Plot the figure of EIF2AK2 cg17326313"
[1] "Plot the figure of IFI44L cg00855901"
[1] "Plot the figure of TTC39C cg18719665"
[1] "Plot the figure of HELZ2 cg06064964"
[1] "Plot the figure of IFI44L cg17980508"
[1] "Plot the figure of HELZ2 cg17593958"
[1] "Plot the figure of HELZ2 cg09844573"
[1] "Plot the figure of HELZ2 cg11779113"
[1] "Plot the figure of IFI44L cg03607951"
3.2.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
3.2.4.1 Table 14: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
| Gene | Pos | Mean.CD8.dc | Mean.CD8.lc | P.value.CD8.dc.lc | FDR | Cgname | |
|---|---|---|---|---|---|---|---|
| 5 | COX7A2 | 75953853 | 0.1791361 | 0.2458823 | 0.0403777 | 0.4625642 | cg06809298 |
| 6 | COX7A2 | 75953935 | 0.0983593 | 0.1268532 | 0.0403777 | 0.4625642 | cg19367436 |
| 26 | PARP9 | 122281939 | 0.7752162 | 0.7061277 | 0.0496820 | 0.4625642 | cg08122652 |
| 9 | HLA-DPB1 | 33048291 | 0.8440094 | 0.8994094 | 0.0497442 | 0.4625642 | cg25045942 |
| 50 | HLA-DPB1 | 33048555 | 0.8772847 | 0.9187396 | 0.0503863 | 0.4625642 | cg19990651 |
| 31 | COX7A2 | 75954053 | 0.6152673 | 0.7003826 | 0.0529465 | 0.4625642 | cg25716013 |
| 27 | PARP9 | 122281975 | 0.5038614 | 0.4227211 | 0.0568061 | 0.4625642 | cg00959259 |
| 1 | MX1 | 42798747 | 0.0767360 | 0.0649603 | 0.0803430 | 0.5204622 | cg08924203 |
| 8 | HLA-DPB1 | 33048286 | 0.8158911 | 0.8756058 | 0.0899516 | 0.5204622 | cg09234582 |
| 7 | SMAD3 | 67361773 | 0.6526138 | 0.4988609 | 0.0917468 | 0.5204622 | cg24961286 |
| 10 | HLA-DPB1 | 33048310 | 0.8029228 | 0.8638414 | 0.1004401 | 0.5204622 | cg13349035 |
| 24 | IFITM1 | 313354 | 0.2827623 | 0.2552977 | 0.1242443 | 0.5901604 | cg11694510 |
| 53 | IFI44L | 79085713 | 0.7196792 | 0.6668886 | 0.1559242 | 0.6836677 | cg17980508 |
| 52 | IFI44L | 79085586 | 0.7342337 | 0.6950998 | 0.1915700 | 0.7340673 | cg03607951 |
| 36 | GFPT2 | 179741121 | 0.6758027 | 0.5892757 | 0.1931756 | 0.7340673 | cg02891314 |
| 47 | HLA-DPB1 | 33048502 | 0.9052612 | 0.9377699 | 0.2120866 | 0.7555585 | cg26645432 |
| 42 | FAM132A | 1178246 | 0.7904919 | 0.6509604 | 0.2313265 | 0.7756242 | cg24345856 |
| 37 | GFPT2 | 179741105 | 0.6153956 | 0.5453461 | 0.2522421 | 0.7987666 | cg23248424 |
| 35 | HELZ2 | 62199190 | 0.0282865 | 0.0368130 | 0.2769422 | 0.8150000 | cg09844573 |
| 41 | GFPT2 | 179740915 | 0.6764403 | 0.6056963 | 0.2859649 | 0.8150000 | cg13944838 |
| 15 | RNF39 | 30039408 | 0.2907931 | 0.2681428 | 0.3225341 | 0.8571533 | cg07382347 |
| 38 | EIF2AK2 | 37383568 | 0.1523055 | 0.1283398 | 0.3464354 | 0.8571533 | cg17326313 |
| 56 | UPK3B | 76145673 | 0.6591430 | 0.6379558 | 0.3484969 | 0.8571533 | cg05372444 |
| 54 | IFI44L | 79085765 | 0.5381196 | 0.5013530 | 0.3609066 | 0.8571533 | cg00855901 |
| 51 | HLA-DPB1 | 33048558 | 0.8637292 | 0.8953533 | 0.3870911 | 0.8825678 | cg01132696 |
| 32 | HELZ2 | 62199034 | 0.1303204 | 0.1507004 | 0.4171925 | 0.9146142 | cg17593958 |
| 2 | RNF39 | 30039142 | 0.1778969 | 0.1987107 | 0.4525638 | 0.9297820 | cg00947782 |
| 55 | IFITM1 | 312518 | 0.0638008 | 0.0545476 | 0.5255517 | 0.9297820 | cg05432003 |
| 19 | RNF39 | 30039466 | 0.2486829 | 0.2344922 | 0.5513504 | 0.9297820 | cg16078649 |
| 39 | TLR1 | 38805732 | 0.2455374 | 0.1967748 | 0.6064685 | 0.9297820 | cg02016764 |
| 25 | HOOK2 | 12877188 | 0.3175145 | 0.3324504 | 0.6142730 | 0.9297820 | cg23899408 |
| 16 | RNF39 | 30039432 | 0.5015302 | 0.4813039 | 0.6173306 | 0.9297820 | cg13401893 |
| 43 | BRDT | 92417998 | 0.4218728 | 0.4340296 | 0.6173306 | 0.9297820 | cg01081438 |
| 45 | HLA-DPB1 | 33048483 | 0.9137198 | 0.9151426 | 0.6196804 | 0.9297820 | cg03229061 |
| 57 | UPK3B | 76145633 | 0.6889555 | 0.7039606 | 0.6226125 | 0.9297820 | cg16453056 |
| 12 | RNF39 | 30039376 | 0.2454873 | 0.2483960 | 0.6355221 | 0.9297820 | cg15877520 |
| 23 | TTC39C | 21572623 | 0.3483870 | 0.3654550 | 0.6493002 | 0.9297820 | cg12639429 |
| 14 | RNF39 | 30039403 | 0.4428490 | 0.4325441 | 0.6539311 | 0.9297820 | cg09279736 |
| 33 | HELZ2 | 62199156 | 0.0183079 | 0.0246032 | 0.6596025 | 0.9297820 | cg11779113 |
| 46 | HLA-DPB1 | 33048485 | 0.8731776 | 0.8895422 | 0.6705576 | 0.9297820 | cg17588455 |
| 21 | TTC39C | 21572657 | 0.1751158 | 0.1911325 | 0.6851025 | 0.9297820 | cg18719665 |
| 40 | HOOK2 | 12877001 | 0.2404004 | 0.2614503 | 0.6851025 | 0.9297820 | cg11738485 |
| 11 | RNF39 | 30039374 | 0.2511929 | 0.2418272 | 0.7103662 | 0.9318861 | cg20249327 |
| 44 | HLA-DPB1 | 33048469 | 0.8301764 | 0.8502348 | 0.7443168 | 0.9318861 | cg10850215 |
| 22 | TTC39C | 21572635 | 0.3737943 | 0.3874764 | 0.7587485 | 0.9318861 | cg05401069 |
| 13 | RNF39 | 30039380 | 0.2266518 | 0.2254552 | 0.7658032 | 0.9318861 | cg13918754 |
| 17 | RNF39 | 30039435 | 0.4492864 | 0.4436087 | 0.7683973 | 0.9318861 | cg12633154 |
| 49 | HLA-DPB1 | 33048540 | 0.8913260 | 0.9024238 | 0.7902422 | 0.9368355 | cg14870156 |
| 48 | HLA-DPB1 | 33048529 | 0.8844981 | 0.9066260 | 0.8118948 | 0.9368355 | cg06437840 |
| 4 | RNF39 | 30039175 | 0.3676492 | 0.3689150 | 0.8459705 | 0.9368355 | cg03343571 |
| 28 | BRDT | 92414722 | 0.3375056 | 0.3259197 | 0.8477344 | 0.9368355 | cg14732540 |
| 20 | RNF39 | 30039476 | 0.3027517 | 0.3066752 | 0.8678401 | 0.9368355 | cg10930308 |
| 34 | HELZ2 | 62199181 | 0.0403199 | 0.0482206 | 0.8710926 | 0.9368355 | cg06064964 |
| 29 | BRDT | 92414737 | 0.4350134 | 0.4226780 | 0.8880295 | 0.9373645 | cg13299824 |
| 30 | BRDT | 92414782 | 0.5136856 | 0.5162384 | 0.9586838 | 0.9897883 | cg02935097 |
| 3 | RNF39 | 30039151 | 0.1489598 | 0.1563919 | 0.9897883 | 0.9897883 | cg18930910 |
| 18 | RNF39 | 30039442 | 0.5503101 | 0.5605175 | 0.9897883 | 0.9897883 | cg10568066 |
3.2.4.2 Figure12: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 12 in our analysis."
3.3 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD4+
3.3.1 Validation of differential methylated CpGsites between SSc patients and Controls
3.3.1.1 Table 14: The Differential methylated CpGsites between SSc patients and Controls
| Gene | Pos | Mean.CD4.SSc | Mean.CD4.NC | P.value.CD4.SSC.NC | FDR | |
|---|---|---|---|---|---|---|
| 51 | IFITM1 | 313408 | 0.1955548 | 0.2401521 | 0.0000949 | 0.0146091 |
| 11 | MX1 | 42798829 | 0.1168171 | 0.1497797 | 0.0011679 | 0.0899277 |
| 128 | FAM132A | 1178105 | 0.9777073 | 0.9809027 | 0.0025672 | 0.0921532 |
| 76 | EIF2AK2 | 37383588 | 0.0711415 | 0.0929983 | 0.0025984 | 0.0921532 |
| 14 | MX1 | 42798857 | 0.1503967 | 0.1895065 | 0.0029920 | 0.0921532 |
| 15 | MX1 | 42798863 | 0.1674460 | 0.2113965 | 0.0042052 | 0.1079333 |
| 5 | MX1 | 42798749 | 0.0286869 | 0.0338268 | 0.0054003 | 0.1188066 |
| 122 | FAM132A | 1178182 | 0.7938068 | 0.8086350 | 0.0068399 | 0.1206740 |
| 123 | FAM132A | 1178172 | 0.8643950 | 0.8761917 | 0.0070524 | 0.1206740 |
| 1 | MX1 | 42798695 | 0.0338730 | 0.0390410 | 0.0082350 | 0.1268184 |
| 9 | MX1 | 42798816 | 0.1304322 | 0.1608932 | 0.0099131 | 0.1371737 |
| 2 | MX1 | 42798698 | 0.0282268 | 0.0316677 | 0.0106889 | 0.1371737 |
| 13 | MX1 | 42798847 | 0.1282379 | 0.1568913 | 0.0119716 | 0.1418178 |
| 80 | EIF2AK2 | 37383730 | 0.0253558 | 0.0313496 | 0.0163700 | 0.1664561 |
| 12 | MX1 | 42798837 | 0.0746994 | 0.0905090 | 0.0171172 | 0.1664561 |
| 78 | EIF2AK2 | 37383679 | 0.0158425 | 0.0179496 | 0.0172941 | 0.1664561 |
| 4 | MX1 | 42798733 | 0.0331928 | 0.0377474 | 0.0206115 | 0.1867161 |
| 7 | MX1 | 42798781 | 0.0654812 | 0.0746964 | 0.0309712 | 0.2572960 |
| 10 | MX1 | 42798818 | 0.0810102 | 0.0970545 | 0.0317443 | 0.2572960 |
| 34 | SMAD3 | 67361798 | 0.9060494 | 0.8799748 | 0.0362919 | 0.2794477 |
| 6 | MX1 | 42798765 | 0.0289796 | 0.0330338 | 0.0413520 | 0.3032482 |
| 3 | MX1 | 42798723 | 0.0486544 | 0.0540432 | 0.0487092 | 0.3399600 |
| 151 | UPK3B | 76145628 | 0.7230687 | 0.7463902 | 0.0507732 | 0.3399600 |
| 8 | MX1 | 42798813 | 0.1292800 | 0.1508762 | 0.0610138 | 0.3846584 |
| 27 | RNF39 | 30039239 | 0.3312149 | 0.3015051 | 0.0624445 | 0.3846584 |
| 120 | FAM132A | 1178202 | 0.7812274 | 0.7903459 | 0.0702747 | 0.4162423 |
| 60 | BRDT | 92414661 | 0.5202705 | 0.5484402 | 0.0871049 | 0.4968208 |
| 124 | FAM132A | 1178162 | 0.8109639 | 0.8198598 | 0.1048672 | 0.5767696 |
| 63 | BRDT | 92414770 | 0.7353634 | 0.7569150 | 0.1373808 | 0.7148964 |
| 119 | FAM132A | 1178207 | 0.8465924 | 0.8540344 | 0.1522422 | 0.7148964 |
| 30 | COX7A2 | 75953883 | 0.1743206 | 0.1921192 | 0.1530608 | 0.7148964 |
| 61 | BRDT | 92414719 | 0.3010934 | 0.3236102 | 0.1572996 | 0.7148964 |
| 24 | RNF39 | 30039208 | 0.1624442 | 0.1495977 | 0.1661652 | 0.7148964 |
| 68 | HELZ2 | 62199061 | 0.0411729 | 0.0312027 | 0.1669424 | 0.7148964 |
| 62 | BRDT | 92414751 | 0.7196543 | 0.7433972 | 0.1722787 | 0.7148964 |
| 130 | BRDT | 92418017 | 0.9711326 | 0.9729621 | 0.1742732 | 0.7148964 |
| 47 | RNF39 | 30039364 | 0.1061779 | 0.0955109 | 0.1785568 | 0.7148964 |
| 64 | BRDT | 92414793 | 0.8163762 | 0.8339878 | 0.1807333 | 0.7148964 |
| 150 | UPK3B | 76145689 | 0.3547661 | 0.3694151 | 0.1810452 | 0.7148964 |
| 56 | HOOK2 | 12877215 | 0.2840337 | 0.3121684 | 0.1901034 | 0.7237129 |
| 145 | IFITM1 | 312434 | 0.1630115 | 0.1794032 | 0.1926768 | 0.7237129 |
| 20 | RNF39 | 30039158 | 0.1156256 | 0.1093117 | 0.2076499 | 0.7613831 |
| 58 | HOOK2 | 12877276 | 0.2752086 | 0.3066603 | 0.2175675 | 0.7650575 |
| 94 | HOOK2 | 12876911 | 0.2828709 | 0.3201762 | 0.2248536 | 0.7650575 |
| 50 | RNF39 | 30039418 | 0.4570728 | 0.4976985 | 0.2258832 | 0.7650575 |
| 33 | COX7A2 | 75953974 | 0.2202770 | 0.2413041 | 0.2287168 | 0.7650575 |
| 59 | BRDT | 92414650 | 0.3998200 | 0.4164258 | 0.2334916 | 0.7650575 |
| 77 | EIF2AK2 | 37383623 | 0.0138249 | 0.0167856 | 0.2412769 | 0.7740969 |
| 153 | UPK3B | 76145606 | 0.3855753 | 0.3740667 | 0.2747625 | 0.8217816 |
| 146 | IFITM1 | 312463 | 0.1262688 | 0.1426939 | 0.2784136 | 0.8217816 |
| 57 | HOOK2 | 12877235 | 0.3330295 | 0.3619532 | 0.2806918 | 0.8217816 |
| 148 | UPK3B | 76145702 | 0.2904265 | 0.3040766 | 0.3009317 | 0.8217816 |
| 29 | COX7A2 | 75953829 | 0.1618291 | 0.1724741 | 0.3224437 | 0.8217816 |
| 35 | SMAD3 | 67361821 | 0.8945688 | 0.8890964 | 0.3291888 | 0.8217816 |
| 121 | FAM132A | 1178192 | 0.9283847 | 0.9309795 | 0.3360343 | 0.8217816 |
| 42 | RNF39 | 30039307 | 0.1850312 | 0.2300563 | 0.3440129 | 0.8217816 |
| 79 | EIF2AK2 | 37383713 | 0.0101216 | 0.0106117 | 0.3459727 | 0.8217816 |
| 55 | HOOK2 | 12877201 | 0.3077689 | 0.3345829 | 0.3550682 | 0.8217816 |
| 65 | COX7A2 | 75954022 | 0.5263550 | 0.5549263 | 0.3612235 | 0.8217816 |
| 28 | COX7A2 | 75953821 | 0.0619963 | 0.0654486 | 0.3638846 | 0.8217816 |
| 32 | COX7A2 | 75953960 | 0.1931812 | 0.2027426 | 0.3645119 | 0.8217816 |
| 88 | HOOK2 | 12876946 | 0.2456540 | 0.2807895 | 0.3754273 | 0.8217816 |
| 17 | RNF39 | 30039127 | 0.3283798 | 0.3144216 | 0.3768842 | 0.8217816 |
| 37 | HLA-DPB1 | 33048370 | 0.6899866 | 0.7210373 | 0.3801472 | 0.8217816 |
| 149 | UPK3B | 76145693 | 0.5299942 | 0.5369975 | 0.3864734 | 0.8217816 |
| 41 | RNF39 | 30039303 | 0.1976302 | 0.2418742 | 0.3875510 | 0.8217816 |
| 125 | FAM132A | 1178150 | 0.9169066 | 0.9182135 | 0.3963196 | 0.8217816 |
| 154 | UPK3B | 76145589 | 0.1747223 | 0.1647508 | 0.4106594 | 0.8217816 |
| 93 | HOOK2 | 12876918 | 0.2633712 | 0.2971163 | 0.4237725 | 0.8217816 |
| 143 | IFI44L | 79085647 | 0.1163383 | 0.1218025 | 0.4240147 | 0.8217816 |
| 22 | RNF39 | 30039202 | 0.1638384 | 0.1512972 | 0.4241843 | 0.8217816 |
| 67 | COX7A2 | 75954122 | 0.4190122 | 0.4398731 | 0.4320049 | 0.8217816 |
| 99 | GFPT2 | 179740970 | 0.5587564 | 0.5300324 | 0.4406541 | 0.8217816 |
| 100 | GFPT2 | 179740963 | 0.6233814 | 0.5924331 | 0.4521171 | 0.8217816 |
| 75 | GFPT2 | 179741039 | 0.5830682 | 0.5537992 | 0.4671794 | 0.8217816 |
| 71 | GFPT2 | 179741067 | 0.5383177 | 0.5113622 | 0.4731907 | 0.8217816 |
| 95 | GFPT2 | 179741008 | 0.5286138 | 0.5032499 | 0.4755354 | 0.8217816 |
| 16 | RNF39 | 30039123 | 0.3791472 | 0.3629646 | 0.4801742 | 0.8217816 |
| 49 | RNF39 | 30039415 | 0.2359129 | 0.2553079 | 0.4853385 | 0.8217816 |
| 69 | GFPT2 | 179741101 | 0.5746154 | 0.5434945 | 0.4976512 | 0.8217816 |
| 73 | GFPT2 | 179741060 | 0.5947270 | 0.5650352 | 0.5038686 | 0.8217816 |
| 89 | HOOK2 | 12876944 | 0.2477893 | 0.2838409 | 0.5057098 | 0.8217816 |
| 98 | GFPT2 | 179740992 | 0.6001045 | 0.5708047 | 0.5057098 | 0.8217816 |
| 45 | RNF39 | 30039349 | 0.2009290 | 0.2340406 | 0.5080327 | 0.8217816 |
| 44 | RNF39 | 30039323 | 0.2805337 | 0.3194670 | 0.5080353 | 0.8217816 |
| 97 | GFPT2 | 179740994 | 0.6138890 | 0.5845215 | 0.5368514 | 0.8217816 |
| 107 | GFPT2 | 179740906 | 0.6369850 | 0.6065319 | 0.5368514 | 0.8217816 |
| 40 | RNF39 | 30039278 | 0.3558052 | 0.3843611 | 0.5399645 | 0.8217816 |
| 70 | GFPT2 | 179741081 | 0.5646860 | 0.5399389 | 0.5420071 | 0.8217816 |
| 96 | GFPT2 | 179740999 | 0.5939736 | 0.5663734 | 0.5431922 | 0.8217816 |
| 102 | GFPT2 | 179740955 | 0.6409681 | 0.6124159 | 0.5431922 | 0.8217816 |
| 104 | GFPT2 | 179740935 | 0.6459324 | 0.6171712 | 0.5431922 | 0.8217816 |
| 137 | HLA-DPB1 | 33048549 | 0.8968477 | 0.9253918 | 0.5473711 | 0.8217816 |
| 101 | GFPT2 | 179740957 | 0.6386792 | 0.6101367 | 0.5624329 | 0.8217816 |
| 105 | GFPT2 | 179740920 | 0.5982046 | 0.5698056 | 0.5624329 | 0.8217816 |
| 66 | COX7A2 | 75954118 | 0.4623212 | 0.4781793 | 0.5628955 | 0.8217816 |
| 74 | GFPT2 | 179741042 | 0.4431661 | 0.4191338 | 0.5681999 | 0.8217816 |
| 126 | FAM132A | 1178136 | 0.9709623 | 0.9725677 | 0.5681999 | 0.8217816 |
| 87 | HOOK2 | 12876948 | 0.2486727 | 0.2842421 | 0.5689180 | 0.8217816 |
| 36 | SMAD3 | 67361896 | 0.8394041 | 0.8322659 | 0.5695113 | 0.8217816 |
| 83 | HOOK2 | 12876997 | 0.2241197 | 0.2582667 | 0.5754383 | 0.8217816 |
| 108 | GFPT2 | 179740900 | 0.5975451 | 0.5676209 | 0.5754383 | 0.8217816 |
| 127 | FAM132A | 1178118 | 0.9508636 | 0.9528701 | 0.5762065 | 0.8217816 |
| 133 | HLA-DPB1 | 33048433 | 0.8975962 | 0.9242818 | 0.5790187 | 0.8217816 |
| 92 | HOOK2 | 12876926 | 0.2523331 | 0.2876337 | 0.5819932 | 0.8217816 |
| 103 | GFPT2 | 179740940 | 0.6012562 | 0.5719450 | 0.5819932 | 0.8217816 |
| 141 | HLA-DPB1 | 33048592 | 0.9197516 | 0.9436297 | 0.5824403 | 0.8217816 |
| 86 | HOOK2 | 12876969 | 0.2424377 | 0.2782543 | 0.5885823 | 0.8217816 |
| 152 | UPK3B | 76145620 | 0.8057483 | 0.8004547 | 0.5899746 | 0.8217816 |
| 31 | COX7A2 | 75953937 | 0.1017073 | 0.1035921 | 0.5946883 | 0.8217816 |
| 43 | RNF39 | 30039313 | 0.2146751 | 0.2466175 | 0.5998517 | 0.8217816 |
| 129 | FAM132A | 1178086 | 0.9187048 | 0.9190379 | 0.5998517 | 0.8217816 |
| 117 | GFPT2 | 179740825 | 0.7377502 | 0.7123661 | 0.6085513 | 0.8217816 |
| 23 | RNF39 | 30039206 | 0.1358605 | 0.1264953 | 0.6101158 | 0.8217816 |
| 135 | HLA-DPB1 | 33048542 | 0.0583057 | 0.0588600 | 0.6136680 | 0.8217816 |
| 114 | GFPT2 | 179740852 | 0.6996409 | 0.6786374 | 0.6220274 | 0.8257949 |
| 109 | GFPT2 | 179740888 | 0.5905199 | 0.5590831 | 0.6356299 | 0.8352430 |
| 110 | GFPT2 | 179740869 | 0.6988038 | 0.6738677 | 0.6493550 | 0.8352430 |
| 139 | HLA-DPB1 | 33048575 | 0.9134333 | 0.9383515 | 0.6509926 | 0.8352430 |
| 54 | HOOK2 | 12877138 | 0.2702749 | 0.2930451 | 0.6562624 | 0.8352430 |
| 106 | GFPT2 | 179740918 | 0.6198811 | 0.5948481 | 0.6562624 | 0.8352430 |
| 38 | RNF39 | 30039271 | 0.1960425 | 0.2340739 | 0.6713819 | 0.8447493 |
| 115 | GFPT2 | 179740840 | 0.7194545 | 0.6979930 | 0.6771574 | 0.8447493 |
| 53 | HOOK2 | 12877107 | 0.2480657 | 0.2701639 | 0.6841783 | 0.8447493 |
| 72 | GFPT2 | 179741063 | 0.5387418 | 0.5144854 | 0.6856731 | 0.8447493 |
| 113 | GFPT2 | 179740855 | 0.7409110 | 0.7204086 | 0.6912264 | 0.8448323 |
| 147 | UPK3B | 76145717 | 0.4342985 | 0.4410031 | 0.7110318 | 0.8556371 |
| 112 | GFPT2 | 179740861 | 0.7174508 | 0.6963664 | 0.7125277 | 0.8556371 |
| 25 | RNF39 | 30039232 | 0.1983630 | 0.1933329 | 0.7167350 | 0.8556371 |
| 84 | HOOK2 | 12876993 | 0.2338669 | 0.2672557 | 0.7268540 | 0.8610424 |
| 90 | HOOK2 | 12876942 | 0.2502241 | 0.2861320 | 0.7557871 | 0.8790559 |
| 91 | HOOK2 | 12876937 | 0.2422273 | 0.2769211 | 0.7630755 | 0.8790559 |
| 116 | GFPT2 | 179740832 | 0.7361678 | 0.7171415 | 0.7630755 | 0.8790559 |
| 81 | TLR1 | 38805839 | 0.0536032 | 0.0543074 | 0.7648928 | 0.8790559 |
| 52 | HOOK2 | 12877099 | 0.2461531 | 0.2670255 | 0.7777140 | 0.8871700 |
| 111 | GFPT2 | 179740867 | 0.6858757 | 0.6670694 | 0.7850629 | 0.8889683 |
| 21 | RNF39 | 30039186 | 0.1412413 | 0.1364882 | 0.7987598 | 0.8925497 |
| 82 | HOOK2 | 12877020 | 0.2328244 | 0.2684078 | 0.7998172 | 0.8925497 |
| 39 | RNF39 | 30039274 | 0.2159565 | 0.2529471 | 0.8111903 | 0.8987288 |
| 142 | HLA-DPB1 | 33048602 | 0.5428538 | 0.5777344 | 0.8181502 | 0.8999652 |
| 46 | RNF39 | 30039354 | 0.2312497 | 0.2679622 | 0.8330229 | 0.9094062 |
| 132 | HLA-DPB1 | 33048423 | 0.9086892 | 0.9338485 | 0.8385433 | 0.9094062 |
| 134 | HLA-DPB1 | 33048444 | 0.8681408 | 0.8946963 | 0.8541111 | 0.9198119 |
| 118 | GFPT2 | 179740822 | 0.7016392 | 0.6859685 | 0.8670164 | 0.9272259 |
| 144 | IFITM1 | 312419 | 0.0662380 | 0.0582821 | 0.9342208 | 0.9798859 |
| 85 | HOOK2 | 12876987 | 0.2393534 | 0.2738826 | 0.9351801 | 0.9798859 |
| 136 | HLA-DPB1 | 33048544 | 0.9186744 | 0.9400067 | 0.9402342 | 0.9798859 |
| 19 | RNF39 | 30039132 | 0.0991727 | 0.1029618 | 0.9417085 | 0.9798859 |
| 48 | RNF39 | 30039411 | 0.4280441 | 0.4423376 | 0.9569891 | 0.9891029 |
| 140 | HLA-DPB1 | 33048581 | 0.9028995 | 0.9264820 | 0.9681035 | 0.9920238 |
| 18 | RNF39 | 30039130 | 0.1580897 | 0.1545091 | 0.9765315 | 0.9920238 |
| 26 | RNF39 | 30039235 | 0.1493717 | 0.1443090 | 0.9843528 | 0.9920238 |
| 131 | HLA-DPB1 | 33048417 | 0.8914680 | 0.9188951 | 0.9881057 | 0.9920238 |
| 138 | HLA-DPB1 | 33048571 | 0.9124444 | 0.9370998 | 0.9920238 | 0.9920238 |
3.3.1.2 Figure12: The Differential methylated CpGsites between SSc patients and Controls
[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD4+ T cells is 1"
[1] "Plot the figure of IFITM1 313408"
3.3.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
3.3.2.1 Table 15: The Differential methylated CpGsites between dcSSc patients and Controls
| Gene | Pos | Mean.CD4.dc | Mean.CD4.NC | P.value.CD4.dc.NC | FDR | |
|---|---|---|---|---|---|---|
| 28 | COX7A2 | 75953821 | 0.0446434 | 0.0654486 | 0.0014698 | 0.1859804 |
| 30 | COX7A2 | 75953883 | 0.1399584 | 0.1921192 | 0.0024153 | 0.1859804 |
| 151 | UPK3B | 76145628 | 0.7062744 | 0.7463902 | 0.0045330 | 0.2326928 |
| 65 | COX7A2 | 75954022 | 0.4518312 | 0.5549263 | 0.0065018 | 0.2503208 |
| 29 | COX7A2 | 75953829 | 0.1264856 | 0.1724741 | 0.0082136 | 0.2529792 |
| 123 | FAM132A | 1178172 | 0.8628519 | 0.8761917 | 0.0103875 | 0.2666113 |
| 32 | COX7A2 | 75953960 | 0.1555675 | 0.2027426 | 0.0188227 | 0.3651751 |
| 31 | COX7A2 | 75953937 | 0.0805141 | 0.1035921 | 0.0213414 | 0.3651751 |
| 33 | COX7A2 | 75953974 | 0.1823139 | 0.2413041 | 0.0213414 | 0.3651751 |
| 122 | FAM132A | 1178182 | 0.7929911 | 0.8086350 | 0.0244646 | 0.3767549 |
| 66 | COX7A2 | 75954118 | 0.4110438 | 0.4781793 | 0.0298290 | 0.4018708 |
| 67 | COX7A2 | 75954122 | 0.3666147 | 0.4398731 | 0.0313146 | 0.4018708 |
| 76 | EIF2AK2 | 37383588 | 0.0759636 | 0.0929983 | 0.0340806 | 0.4037239 |
| 78 | EIF2AK2 | 37383679 | 0.0143214 | 0.0179496 | 0.0393835 | 0.4332186 |
| 37 | HLA-DPB1 | 33048370 | 0.6273491 | 0.7210373 | 0.0737282 | 0.7037514 |
| 139 | HLA-DPB1 | 33048575 | 0.8728620 | 0.9383515 | 0.0763787 | 0.7037514 |
| 51 | IFITM1 | 313408 | 0.2193774 | 0.2401521 | 0.0865762 | 0.7037514 |
| 34 | SMAD3 | 67361798 | 0.9058747 | 0.8799748 | 0.0953294 | 0.7037514 |
| 128 | FAM132A | 1178105 | 0.9789670 | 0.9809027 | 0.0972014 | 0.7037514 |
| 80 | EIF2AK2 | 37383730 | 0.0263226 | 0.0313496 | 0.1109068 | 0.7037514 |
| 4 | MX1 | 42798733 | 0.0346634 | 0.0377474 | 0.1262778 | 0.7037514 |
| 136 | HLA-DPB1 | 33048544 | 0.8773159 | 0.9400067 | 0.1272663 | 0.7037514 |
| 133 | HLA-DPB1 | 33048433 | 0.8554437 | 0.9242818 | 0.1433082 | 0.7037514 |
| 11 | MX1 | 42798829 | 0.1365556 | 0.1497797 | 0.1559733 | 0.7037514 |
| 135 | HLA-DPB1 | 33048542 | 0.0683155 | 0.0588600 | 0.1581536 | 0.7037514 |
| 94 | HOOK2 | 12876911 | 0.2628716 | 0.3201762 | 0.1669421 | 0.7037514 |
| 21 | RNF39 | 30039186 | 0.1254795 | 0.1364882 | 0.1702702 | 0.7037514 |
| 14 | MX1 | 42798857 | 0.1718197 | 0.1895065 | 0.1708868 | 0.7037514 |
| 58 | HOOK2 | 12877276 | 0.2590516 | 0.3066603 | 0.1784679 | 0.7037514 |
| 5 | MX1 | 42798749 | 0.0309253 | 0.0338268 | 0.1905622 | 0.7037514 |
| 138 | HLA-DPB1 | 33048571 | 0.8724026 | 0.9370998 | 0.2077564 | 0.7037514 |
| 42 | RNF39 | 30039307 | 0.1733708 | 0.2300563 | 0.2178187 | 0.7037514 |
| 50 | RNF39 | 30039418 | 0.4442470 | 0.4976985 | 0.2248090 | 0.7037514 |
| 142 | HLA-DPB1 | 33048602 | 0.4494760 | 0.5777344 | 0.2253595 | 0.7037514 |
| 148 | UPK3B | 76145702 | 0.2841578 | 0.3040766 | 0.2348383 | 0.7037514 |
| 15 | MX1 | 42798863 | 0.1933493 | 0.2113965 | 0.2448278 | 0.7037514 |
| 137 | HLA-DPB1 | 33048549 | 0.8561483 | 0.9253918 | 0.2468203 | 0.7037514 |
| 79 | EIF2AK2 | 37383713 | 0.0083365 | 0.0106117 | 0.2480905 | 0.7037514 |
| 18 | RNF39 | 30039130 | 0.1422862 | 0.1545091 | 0.2505736 | 0.7037514 |
| 27 | RNF39 | 30039239 | 0.3243063 | 0.3015051 | 0.2544149 | 0.7037514 |
| 120 | FAM132A | 1178202 | 0.7827009 | 0.7903459 | 0.2652243 | 0.7037514 |
| 56 | HOOK2 | 12877215 | 0.2709562 | 0.3121684 | 0.2676775 | 0.7037514 |
| 13 | MX1 | 42798847 | 0.1465303 | 0.1568913 | 0.2756029 | 0.7037514 |
| 19 | RNF39 | 30039132 | 0.0922963 | 0.1029618 | 0.2898598 | 0.7037514 |
| 57 | HOOK2 | 12877235 | 0.3206069 | 0.3619532 | 0.2919194 | 0.7037514 |
| 124 | FAM132A | 1178162 | 0.8130103 | 0.8198598 | 0.3070953 | 0.7037514 |
| 119 | FAM132A | 1178207 | 0.8479868 | 0.8540344 | 0.3080908 | 0.7037514 |
| 54 | HOOK2 | 12877138 | 0.2542766 | 0.2930451 | 0.3088587 | 0.7037514 |
| 117 | GFPT2 | 179740825 | 0.7798747 | 0.7123661 | 0.3088587 | 0.7037514 |
| 141 | HLA-DPB1 | 33048592 | 0.8785906 | 0.9436297 | 0.3199569 | 0.7037514 |
| 44 | RNF39 | 30039323 | 0.2670671 | 0.3194670 | 0.3214626 | 0.7037514 |
| 60 | BRDT | 92414661 | 0.5263980 | 0.5484402 | 0.3249814 | 0.7037514 |
| 144 | IFITM1 | 312419 | 0.0729589 | 0.0582821 | 0.3383131 | 0.7037514 |
| 25 | RNF39 | 30039232 | 0.1782205 | 0.1933329 | 0.3435172 | 0.7037514 |
| 75 | GFPT2 | 179741039 | 0.6135393 | 0.5537992 | 0.3435172 | 0.7037514 |
| 55 | HOOK2 | 12877201 | 0.2941553 | 0.3345829 | 0.3446061 | 0.7037514 |
| 92 | HOOK2 | 12876926 | 0.2325951 | 0.2876337 | 0.3446061 | 0.7037514 |
| 131 | HLA-DPB1 | 33048417 | 0.8528855 | 0.9188951 | 0.3520793 | 0.7037514 |
| 150 | UPK3B | 76145689 | 0.3570678 | 0.3694151 | 0.3539311 | 0.7037514 |
| 52 | HOOK2 | 12877099 | 0.2306115 | 0.2670255 | 0.3634106 | 0.7037514 |
| 132 | HLA-DPB1 | 33048423 | 0.8696502 | 0.9338485 | 0.3719926 | 0.7037514 |
| 49 | RNF39 | 30039415 | 0.2266577 | 0.2553079 | 0.3725329 | 0.7037514 |
| 93 | HOOK2 | 12876918 | 0.2439106 | 0.2971163 | 0.3730440 | 0.7037514 |
| 114 | GFPT2 | 179740852 | 0.7368690 | 0.6786374 | 0.3730440 | 0.7037514 |
| 26 | RNF39 | 30039235 | 0.1358569 | 0.1443090 | 0.3787070 | 0.7037514 |
| 126 | FAM132A | 1178136 | 0.9701882 | 0.9725677 | 0.3825257 | 0.7037514 |
| 2 | MX1 | 42798698 | 0.0308387 | 0.0316677 | 0.3828306 | 0.7037514 |
| 100 | GFPT2 | 179740963 | 0.6543772 | 0.5924331 | 0.3828306 | 0.7037514 |
| 74 | GFPT2 | 179741042 | 0.4692564 | 0.4191338 | 0.3926775 | 0.7037514 |
| 104 | GFPT2 | 179740935 | 0.6806278 | 0.6171712 | 0.3927697 | 0.7037514 |
| 88 | HOOK2 | 12876946 | 0.2254400 | 0.2807895 | 0.4028602 | 0.7037514 |
| 113 | GFPT2 | 179740855 | 0.7807848 | 0.7204086 | 0.4028602 | 0.7037514 |
| 36 | SMAD3 | 67361896 | 0.8435264 | 0.8322659 | 0.4042664 | 0.7037514 |
| 3 | MX1 | 42798723 | 0.0513214 | 0.0540432 | 0.4131011 | 0.7037514 |
| 12 | MX1 | 42798837 | 0.0850276 | 0.0905090 | 0.4131011 | 0.7037514 |
| 110 | GFPT2 | 179740869 | 0.7353703 | 0.6738677 | 0.4131011 | 0.7037514 |
| 41 | RNF39 | 30039303 | 0.1915649 | 0.2418742 | 0.4134546 | 0.7037514 |
| 71 | GFPT2 | 179741067 | 0.5638664 | 0.5113622 | 0.4134546 | 0.7037514 |
| 121 | FAM132A | 1178192 | 0.9283732 | 0.9309795 | 0.4134546 | 0.7037514 |
| 134 | HLA-DPB1 | 33048444 | 0.8251486 | 0.8946963 | 0.4138171 | 0.7037514 |
| 98 | GFPT2 | 179740992 | 0.6312012 | 0.5708047 | 0.4234915 | 0.7037514 |
| 99 | GFPT2 | 179740970 | 0.5854953 | 0.5300324 | 0.4234915 | 0.7037514 |
| 109 | GFPT2 | 179740888 | 0.6252246 | 0.5590831 | 0.4234915 | 0.7037514 |
| 115 | GFPT2 | 179740840 | 0.7598012 | 0.6979930 | 0.4234915 | 0.7037514 |
| 116 | GFPT2 | 179740832 | 0.7763586 | 0.7171415 | 0.4234915 | 0.7037514 |
| 140 | HLA-DPB1 | 33048581 | 0.8656858 | 0.9264820 | 0.4262430 | 0.7037514 |
| 102 | GFPT2 | 179740955 | 0.6733490 | 0.6124159 | 0.4340299 | 0.7037514 |
| 112 | GFPT2 | 179740861 | 0.7560015 | 0.6963664 | 0.4340299 | 0.7037514 |
| 53 | HOOK2 | 12877107 | 0.2337943 | 0.2701639 | 0.4447151 | 0.7037514 |
| 101 | GFPT2 | 179740957 | 0.6711285 | 0.6101367 | 0.4447151 | 0.7037514 |
| 118 | GFPT2 | 179740822 | 0.7419350 | 0.6859685 | 0.4447151 | 0.7037514 |
| 77 | EIF2AK2 | 37383623 | 0.0132245 | 0.0167856 | 0.4481670 | 0.7037514 |
| 125 | FAM132A | 1178150 | 0.9220973 | 0.9182135 | 0.4529283 | 0.7037514 |
| 40 | RNF39 | 30039278 | 0.3409712 | 0.3843611 | 0.4529365 | 0.7037514 |
| 73 | GFPT2 | 179741060 | 0.6235241 | 0.5650352 | 0.4568674 | 0.7037514 |
| 23 | RNF39 | 30039206 | 0.1187244 | 0.1264953 | 0.4641705 | 0.7037514 |
| 96 | GFPT2 | 179740999 | 0.6234426 | 0.5663734 | 0.4665199 | 0.7037514 |
| 97 | GFPT2 | 179740994 | 0.6448891 | 0.5845215 | 0.4665199 | 0.7037514 |
| 69 | GFPT2 | 179741101 | 0.5996110 | 0.5434945 | 0.4680993 | 0.7037514 |
| 127 | FAM132A | 1178118 | 0.9495490 | 0.9528701 | 0.4698451 | 0.7037514 |
| 91 | HOOK2 | 12876937 | 0.2229114 | 0.2769211 | 0.4776362 | 0.7037514 |
| 95 | GFPT2 | 179741008 | 0.5565324 | 0.5032499 | 0.4888928 | 0.7037514 |
| 61 | BRDT | 92414719 | 0.3078300 | 0.3236102 | 0.4910052 | 0.7037514 |
| 45 | RNF39 | 30039349 | 0.1943104 | 0.2340406 | 0.4987776 | 0.7037514 |
| 9 | MX1 | 42798816 | 0.1525878 | 0.1608932 | 0.5002878 | 0.7037514 |
| 87 | HOOK2 | 12876948 | 0.2287765 | 0.2842421 | 0.5002878 | 0.7037514 |
| 103 | GFPT2 | 179740940 | 0.6335832 | 0.5719450 | 0.5002878 | 0.7037514 |
| 105 | GFPT2 | 179740920 | 0.6286866 | 0.5698056 | 0.5002878 | 0.7037514 |
| 107 | GFPT2 | 179740906 | 0.6711654 | 0.6065319 | 0.5002878 | 0.7037514 |
| 43 | RNF39 | 30039313 | 0.2053626 | 0.2466175 | 0.5106213 | 0.7037514 |
| 89 | HOOK2 | 12876944 | 0.2283631 | 0.2838409 | 0.5118192 | 0.7037514 |
| 108 | GFPT2 | 179740900 | 0.6263760 | 0.5676209 | 0.5118192 | 0.7037514 |
| 7 | MX1 | 42798781 | 0.0723267 | 0.0746964 | 0.5234849 | 0.7134219 |
| 47 | RNF39 | 30039364 | 0.1044725 | 0.0955109 | 0.5385277 | 0.7149419 |
| 70 | GFPT2 | 179741081 | 0.5870507 | 0.5399389 | 0.5385277 | 0.7149419 |
| 72 | GFPT2 | 179741063 | 0.5645206 | 0.5144854 | 0.5385277 | 0.7149419 |
| 1 | MX1 | 42798695 | 0.0381601 | 0.0390410 | 0.5472100 | 0.7202593 |
| 82 | HOOK2 | 12877020 | 0.2123525 | 0.2684078 | 0.5592647 | 0.7219432 |
| 38 | RNF39 | 30039271 | 0.1879945 | 0.2340739 | 0.5631068 | 0.7219432 |
| 6 | MX1 | 42798765 | 0.0317686 | 0.0330338 | 0.5714442 | 0.7219432 |
| 106 | GFPT2 | 179740918 | 0.6526585 | 0.5948481 | 0.5714442 | 0.7219432 |
| 129 | FAM132A | 1178086 | 0.9193654 | 0.9190379 | 0.5719290 | 0.7219432 |
| 111 | GFPT2 | 179740867 | 0.7217714 | 0.6670694 | 0.5837457 | 0.7305105 |
| 62 | BRDT | 92414751 | 0.7326712 | 0.7433972 | 0.5882033 | 0.7305105 |
| 10 | MX1 | 42798818 | 0.0941620 | 0.0970545 | 0.6087041 | 0.7439717 |
| 130 | BRDT | 92418017 | 0.9728535 | 0.9729621 | 0.6087041 | 0.7439717 |
| 153 | UPK3B | 76145606 | 0.3782685 | 0.3740667 | 0.6307751 | 0.7579801 |
| 90 | HOOK2 | 12876942 | 0.2300281 | 0.2861320 | 0.6341167 | 0.7579801 |
| 22 | RNF39 | 30039202 | 0.1501742 | 0.1512972 | 0.6365307 | 0.7579801 |
| 17 | RNF39 | 30039127 | 0.3078670 | 0.3144216 | 0.6398533 | 0.7579801 |
| 83 | HOOK2 | 12876997 | 0.2060073 | 0.2582667 | 0.6599588 | 0.7621717 |
| 147 | UPK3B | 76145717 | 0.4323066 | 0.4410031 | 0.6599588 | 0.7621717 |
| 149 | UPK3B | 76145693 | 0.5311877 | 0.5369975 | 0.6599588 | 0.7621717 |
| 35 | SMAD3 | 67361821 | 0.8864407 | 0.8890964 | 0.6631884 | 0.7621717 |
| 143 | IFI44L | 79085647 | 0.1195439 | 0.1218025 | 0.6709270 | 0.7628837 |
| 68 | HELZ2 | 62199061 | 0.0356405 | 0.0312027 | 0.6751122 | 0.7628837 |
| 81 | TLR1 | 38805839 | 0.0596818 | 0.0543074 | 0.6786693 | 0.7628837 |
| 86 | HOOK2 | 12876969 | 0.2234150 | 0.2782543 | 0.6862044 | 0.7657643 |
| 154 | UPK3B | 76145589 | 0.1720512 | 0.1647508 | 0.7167959 | 0.7926289 |
| 16 | RNF39 | 30039123 | 0.3614561 | 0.3629646 | 0.7205717 | 0.7926289 |
| 146 | IFITM1 | 312463 | 0.1562166 | 0.1426939 | 0.7498587 | 0.8189946 |
| 63 | BRDT | 92414770 | 0.7509697 | 0.7569150 | 0.7597665 | 0.8235646 |
| 152 | UPK3B | 76145620 | 0.7966523 | 0.8004547 | 0.7647386 | 0.8235646 |
| 39 | RNF39 | 30039274 | 0.2086611 | 0.2529471 | 0.7761999 | 0.8301027 |
| 46 | RNF39 | 30039354 | 0.2246827 | 0.2679622 | 0.8044616 | 0.8528366 |
| 8 | MX1 | 42798813 | 0.1528304 | 0.1508762 | 0.8085334 | 0.8528366 |
| 85 | HOOK2 | 12876987 | 0.2186697 | 0.2738826 | 0.8505202 | 0.8910212 |
| 84 | HOOK2 | 12876993 | 0.2152394 | 0.2672557 | 0.8787515 | 0.9143766 |
| 48 | RNF39 | 30039411 | 0.4167763 | 0.4423376 | 0.8894606 | 0.9193083 |
| 59 | BRDT | 92414650 | 0.4258523 | 0.4164258 | 0.9335398 | 0.9571429 |
| 20 | RNF39 | 30039158 | 0.1019108 | 0.1093117 | 0.9482851 | 0.9571429 |
| 24 | RNF39 | 30039208 | 0.1471008 | 0.1495977 | 0.9488318 | 0.9571429 |
| 145 | IFITM1 | 312434 | 0.2057482 | 0.1794032 | 0.9509277 | 0.9571429 |
| 64 | BRDT | 92414793 | 0.8320961 | 0.8339878 | 0.9634393 | 0.9634393 |
3.3.2.2 Figure13: The Differential methylated CpGsites between dcSSc patients and Controls
[1] "As there are no CpGsite showed significant difference between dcSSc patients and controls, there is no Figure 13 in our analysis."
3.3.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
3.3.3.1 Table 16: The Differential methylated CpGsites between dcSSc lcSSc patients and Controls
| Gene | Pos | Mean.CD4.lc | Mean.CD4.NC | P.value.CD4.lc.NC | FDR | |
|---|---|---|---|---|---|---|
| 51 | IFITM1 | 313408 | 0.1796731 | 0.2401521 | 0.0000122 | 0.0018800 |
| 11 | MX1 | 42798829 | 0.1036581 | 0.1497797 | 0.0003040 | 0.0234114 |
| 1 | MX1 | 42798695 | 0.0310149 | 0.0390410 | 0.0007168 | 0.0365720 |
| 15 | MX1 | 42798863 | 0.1501772 | 0.2113965 | 0.0011647 | 0.0365720 |
| 14 | MX1 | 42798857 | 0.1361146 | 0.1895065 | 0.0012631 | 0.0365720 |
| 9 | MX1 | 42798816 | 0.1156618 | 0.1608932 | 0.0014249 | 0.0365720 |
| 128 | FAM132A | 1178105 | 0.9768675 | 0.9809027 | 0.0017163 | 0.0377596 |
| 2 | MX1 | 42798698 | 0.0264856 | 0.0316677 | 0.0024984 | 0.0448923 |
| 5 | MX1 | 42798749 | 0.0271947 | 0.0338268 | 0.0026236 | 0.0448923 |
| 8 | MX1 | 42798813 | 0.1135797 | 0.1508762 | 0.0033381 | 0.0514067 |
| 12 | MX1 | 42798837 | 0.0678139 | 0.0905090 | 0.0048474 | 0.0678641 |
| 13 | MX1 | 42798847 | 0.1160429 | 0.1568913 | 0.0053089 | 0.0681307 |
| 10 | MX1 | 42798818 | 0.0722424 | 0.0970545 | 0.0066373 | 0.0786262 |
| 76 | EIF2AK2 | 37383588 | 0.0681276 | 0.0929983 | 0.0072459 | 0.0797054 |
| 7 | MX1 | 42798781 | 0.0609176 | 0.0746964 | 0.0086127 | 0.0884234 |
| 6 | MX1 | 42798765 | 0.0271204 | 0.0330338 | 0.0125539 | 0.1208314 |
| 3 | MX1 | 42798723 | 0.0468764 | 0.0540432 | 0.0271852 | 0.2325843 |
| 80 | EIF2AK2 | 37383730 | 0.0247515 | 0.0313496 | 0.0271852 | 0.2325843 |
| 122 | FAM132A | 1178182 | 0.7943505 | 0.8086350 | 0.0301499 | 0.2419470 |
| 4 | MX1 | 42798733 | 0.0322124 | 0.0377474 | 0.0314217 | 0.2419470 |
| 145 | IFITM1 | 312434 | 0.1337707 | 0.1794032 | 0.0478549 | 0.3509361 |
| 24 | RNF39 | 30039208 | 0.1726732 | 0.1495977 | 0.0511500 | 0.3580500 |
| 123 | FAM132A | 1178172 | 0.8654238 | 0.8761917 | 0.0546959 | 0.3623529 |
| 63 | BRDT | 92414770 | 0.7249593 | 0.7569150 | 0.0569540 | 0.3623529 |
| 64 | BRDT | 92414793 | 0.8058962 | 0.8339878 | 0.0588235 | 0.3623529 |
| 146 | IFITM1 | 312463 | 0.1053054 | 0.1426939 | 0.0639694 | 0.3757275 |
| 78 | EIF2AK2 | 37383679 | 0.0167932 | 0.0179496 | 0.0658743 | 0.3757275 |
| 27 | RNF39 | 30039239 | 0.3358206 | 0.3015051 | 0.0700346 | 0.3767049 |
| 125 | FAM132A | 1178150 | 0.9134462 | 0.9182135 | 0.0711358 | 0.3767049 |
| 59 | BRDT | 92414650 | 0.3824652 | 0.4164258 | 0.0733841 | 0.3767049 |
| 20 | RNF39 | 30039158 | 0.1247689 | 0.1093117 | 0.0780478 | 0.3811890 |
| 120 | FAM132A | 1178202 | 0.7802450 | 0.7903459 | 0.0804279 | 0.3811890 |
| 34 | SMAD3 | 67361798 | 0.9061659 | 0.8799748 | 0.0816833 | 0.3811890 |
| 60 | BRDT | 92414661 | 0.5161855 | 0.5484402 | 0.0881805 | 0.3994056 |
| 68 | HELZ2 | 62199061 | 0.0448612 | 0.0312027 | 0.0951017 | 0.4184473 |
| 17 | RNF39 | 30039127 | 0.3420550 | 0.3144216 | 0.0994260 | 0.4253225 |
| 141 | HLA-DPB1 | 33048592 | 0.9471922 | 0.9436297 | 0.1185622 | 0.4688546 |
| 130 | BRDT | 92418017 | 0.9699854 | 0.9729621 | 0.1192884 | 0.4688546 |
| 62 | BRDT | 92414751 | 0.7109765 | 0.7433972 | 0.1217804 | 0.4688546 |
| 124 | FAM132A | 1178162 | 0.8095996 | 0.8198598 | 0.1217804 | 0.4688546 |
| 22 | RNF39 | 30039202 | 0.1729478 | 0.1512972 | 0.1281305 | 0.4812707 |
| 61 | BRDT | 92414719 | 0.2966023 | 0.3236102 | 0.1324693 | 0.4857207 |
| 47 | RNF39 | 30039364 | 0.1073149 | 0.0955109 | 0.1438587 | 0.5152149 |
| 23 | RNF39 | 30039206 | 0.1472846 | 0.1264953 | 0.1928652 | 0.6600457 |
| 16 | RNF39 | 30039123 | 0.3909412 | 0.3629646 | 0.1928705 | 0.6600457 |
| 119 | FAM132A | 1178207 | 0.8456628 | 0.8540344 | 0.2018483 | 0.6757531 |
| 25 | RNF39 | 30039232 | 0.2117913 | 0.1933329 | 0.2077654 | 0.6807633 |
| 150 | UPK3B | 76145689 | 0.3532317 | 0.3694151 | 0.2276299 | 0.7238409 |
| 153 | UPK3B | 76145606 | 0.3904465 | 0.3740667 | 0.2303130 | 0.7238409 |
| 77 | EIF2AK2 | 37383623 | 0.0142002 | 0.0167856 | 0.2763252 | 0.8346787 |
| 28 | COX7A2 | 75953821 | 0.0740679 | 0.0654486 | 0.2764196 | 0.8346787 |
| 35 | SMAD3 | 67361821 | 0.8999875 | 0.8890964 | 0.2851982 | 0.8446256 |
| 136 | HLA-DPB1 | 33048544 | 0.9462467 | 0.9400067 | 0.2947441 | 0.8564262 |
| 56 | HOOK2 | 12877215 | 0.2927520 | 0.3121684 | 0.3039772 | 0.8648714 |
| 152 | UPK3B | 76145620 | 0.8118123 | 0.8004547 | 0.3113647 | 0.8648714 |
| 31 | COX7A2 | 75953937 | 0.1164504 | 0.1035921 | 0.3177720 | 0.8648714 |
| 132 | HLA-DPB1 | 33048423 | 0.9347152 | 0.9338485 | 0.3247835 | 0.8648714 |
| 138 | HLA-DPB1 | 33048571 | 0.9391389 | 0.9370998 | 0.3257308 | 0.8648714 |
| 149 | UPK3B | 76145693 | 0.5291985 | 0.5369975 | 0.3673767 | 0.9429335 |
| 154 | UPK3B | 76145589 | 0.1765031 | 0.1647508 | 0.3673767 | 0.9429335 |
| 144 | IFITM1 | 312419 | 0.0619931 | 0.0582821 | 0.4059303 | 0.9946184 |
| 18 | RNF39 | 30039130 | 0.1686253 | 0.1545091 | 0.4105201 | 0.9946184 |
| 143 | IFI44L | 79085647 | 0.1143348 | 0.1218025 | 0.4157401 | 0.9946184 |
| 50 | RNF39 | 30039418 | 0.4656233 | 0.4976985 | 0.4185943 | 0.9946184 |
| 66 | COX7A2 | 75954118 | 0.4965062 | 0.4781793 | 0.4198065 | 0.9946184 |
| 81 | TLR1 | 38805839 | 0.0494588 | 0.0543074 | 0.4418207 | 1.0000000 |
| 121 | FAM132A | 1178192 | 0.9283924 | 0.9309795 | 0.4517972 | 1.0000000 |
| 57 | HOOK2 | 12877235 | 0.3413112 | 0.3619532 | 0.4609924 | 1.0000000 |
| 58 | HOOK2 | 12877276 | 0.2859800 | 0.3066603 | 0.4609924 | 1.0000000 |
| 65 | COX7A2 | 75954022 | 0.5760375 | 0.5549263 | 0.4776318 | 1.0000000 |
| 26 | RNF39 | 30039235 | 0.1583816 | 0.1443090 | 0.4791272 | 1.0000000 |
| 19 | RNF39 | 30039132 | 0.1037569 | 0.1029618 | 0.4864167 | 1.0000000 |
| 94 | HOOK2 | 12876911 | 0.2962037 | 0.3201762 | 0.4952656 | 1.0000000 |
| 131 | HLA-DPB1 | 33048417 | 0.9171898 | 0.9188951 | 0.4952986 | 1.0000000 |
| 139 | HLA-DPB1 | 33048575 | 0.9404808 | 0.9383515 | 0.4952986 | 1.0000000 |
| 21 | RNF39 | 30039186 | 0.1517492 | 0.1364882 | 0.5042415 | 1.0000000 |
| 140 | HLA-DPB1 | 33048581 | 0.9277086 | 0.9264820 | 0.5044426 | 1.0000000 |
| 151 | UPK3B | 76145628 | 0.7342650 | 0.7463902 | 0.5235259 | 1.0000000 |
| 88 | HOOK2 | 12876946 | 0.2591300 | 0.2807895 | 0.5308336 | 1.0000000 |
| 41 | RNF39 | 30039303 | 0.2016737 | 0.2418742 | 0.5408827 | 1.0000000 |
| 55 | HOOK2 | 12877201 | 0.3168446 | 0.3345829 | 0.5490840 | 1.0000000 |
| 29 | COX7A2 | 75953829 | 0.1864159 | 0.1724741 | 0.5594925 | 1.0000000 |
| 142 | HLA-DPB1 | 33048602 | 0.6051056 | 0.5777344 | 0.5610910 | 1.0000000 |
| 148 | UPK3B | 76145702 | 0.2946057 | 0.3040766 | 0.5649388 | 1.0000000 |
| 32 | COX7A2 | 75953960 | 0.2193472 | 0.2027426 | 0.6103232 | 1.0000000 |
| 95 | GFPT2 | 179741008 | 0.5100013 | 0.5032499 | 0.6249850 | 1.0000000 |
| 99 | GFPT2 | 179740970 | 0.5409305 | 0.5300324 | 0.6249850 | 1.0000000 |
| 67 | COX7A2 | 75954122 | 0.4539439 | 0.4398731 | 0.6278239 | 1.0000000 |
| 79 | EIF2AK2 | 37383713 | 0.0112373 | 0.0106117 | 0.6347781 | 1.0000000 |
| 83 | HOOK2 | 12876997 | 0.2361947 | 0.2582667 | 0.6446345 | 1.0000000 |
| 86 | HOOK2 | 12876969 | 0.2551195 | 0.2782543 | 0.6446345 | 1.0000000 |
| 93 | HOOK2 | 12876918 | 0.2763449 | 0.2971163 | 0.6446345 | 1.0000000 |
| 89 | HOOK2 | 12876944 | 0.2607402 | 0.2838409 | 0.6545528 | 1.0000000 |
| 45 | RNF39 | 30039349 | 0.2053414 | 0.2340406 | 0.6659660 | 1.0000000 |
| 42 | RNF39 | 30039307 | 0.1928048 | 0.2300563 | 0.6762892 | 1.0000000 |
| 69 | GFPT2 | 179741101 | 0.5579517 | 0.5434945 | 0.6785338 | 1.0000000 |
| 100 | GFPT2 | 179740963 | 0.6027175 | 0.5924331 | 0.6846640 | 1.0000000 |
| 70 | GFPT2 | 179741081 | 0.5497762 | 0.5399389 | 0.6888596 | 1.0000000 |
| 71 | GFPT2 | 179741067 | 0.5212852 | 0.5113622 | 0.6888596 | 1.0000000 |
| 73 | GFPT2 | 179741060 | 0.5755289 | 0.5650352 | 0.6992427 | 1.0000000 |
| 84 | HOOK2 | 12876993 | 0.2462851 | 0.2672557 | 0.7050196 | 1.0000000 |
| 107 | GFPT2 | 179740906 | 0.6141981 | 0.6065319 | 0.7152770 | 1.0000000 |
| 134 | HLA-DPB1 | 33048444 | 0.8968022 | 0.8946963 | 0.7252828 | 1.0000000 |
| 135 | HLA-DPB1 | 33048542 | 0.0516326 | 0.0588600 | 0.7341313 | 1.0000000 |
| 98 | GFPT2 | 179740992 | 0.5793734 | 0.5708047 | 0.7359427 | 1.0000000 |
| 118 | GFPT2 | 179740822 | 0.6747754 | 0.6859685 | 0.7359427 | 1.0000000 |
| 97 | GFPT2 | 179740994 | 0.5932223 | 0.5845215 | 0.7463476 | 1.0000000 |
| 129 | FAM132A | 1178086 | 0.9182644 | 0.9190379 | 0.7501385 | 1.0000000 |
| 49 | RNF39 | 30039415 | 0.2420830 | 0.2553079 | 0.7519581 | 1.0000000 |
| 75 | GFPT2 | 179741039 | 0.5627541 | 0.5537992 | 0.7519581 | 1.0000000 |
| 133 | HLA-DPB1 | 33048433 | 0.9256979 | 0.9242818 | 0.7560148 | 1.0000000 |
| 96 | GFPT2 | 179740999 | 0.5743277 | 0.5663734 | 0.7567983 | 1.0000000 |
| 105 | GFPT2 | 179740920 | 0.5778832 | 0.5698056 | 0.7567983 | 1.0000000 |
| 40 | RNF39 | 30039278 | 0.3656945 | 0.3843611 | 0.7608970 | 1.0000000 |
| 87 | HOOK2 | 12876948 | 0.2619367 | 0.2842421 | 0.7672930 | 1.0000000 |
| 108 | GFPT2 | 179740900 | 0.5783244 | 0.5676209 | 0.7672930 | 1.0000000 |
| 52 | HOOK2 | 12877099 | 0.2565141 | 0.2670255 | 0.7778298 | 1.0000000 |
| 85 | HOOK2 | 12876987 | 0.2531426 | 0.2738826 | 0.7884070 | 1.0000000 |
| 102 | GFPT2 | 179740955 | 0.6193809 | 0.6124159 | 0.7884070 | 1.0000000 |
| 103 | GFPT2 | 179740940 | 0.5797049 | 0.5719450 | 0.7884070 | 1.0000000 |
| 43 | RNF39 | 30039313 | 0.2208833 | 0.2466175 | 0.8043754 | 1.0000000 |
| 127 | FAM132A | 1178118 | 0.9517401 | 0.9528701 | 0.8058384 | 1.0000000 |
| 101 | GFPT2 | 179740957 | 0.6170463 | 0.6101367 | 0.8096752 | 1.0000000 |
| 30 | COX7A2 | 75953883 | 0.1982248 | 0.1921192 | 0.8190017 | 1.0000000 |
| 104 | GFPT2 | 179740935 | 0.6228022 | 0.6171712 | 0.8310828 | 1.0000000 |
| 106 | GFPT2 | 179740918 | 0.5980296 | 0.5948481 | 0.8418341 | 1.0000000 |
| 44 | RNF39 | 30039323 | 0.2895114 | 0.3194670 | 0.8484676 | 1.0000000 |
| 48 | RNF39 | 30039411 | 0.4355559 | 0.4423376 | 0.8484676 | 1.0000000 |
| 147 | UPK3B | 76145717 | 0.4356264 | 0.4410031 | 0.8514916 | 1.0000000 |
| 36 | SMAD3 | 67361896 | 0.8366558 | 0.8322659 | 0.8595659 | 1.0000000 |
| 116 | GFPT2 | 179740832 | 0.7093739 | 0.7171415 | 0.8634221 | 1.0000000 |
| 38 | RNF39 | 30039271 | 0.2014079 | 0.2340739 | 0.8716915 | 1.0000000 |
| 74 | GFPT2 | 179741042 | 0.4257726 | 0.4191338 | 0.8716915 | 1.0000000 |
| 126 | FAM132A | 1178136 | 0.9714783 | 0.9725677 | 0.8827656 | 1.0000000 |
| 54 | HOOK2 | 12877138 | 0.2809405 | 0.2930451 | 0.8959883 | 1.0000000 |
| 39 | RNF39 | 30039274 | 0.2208201 | 0.2529471 | 0.9049794 | 1.0000000 |
| 46 | RNF39 | 30039354 | 0.2356277 | 0.2679622 | 0.9154616 | 1.0000000 |
| 72 | GFPT2 | 179741063 | 0.5215559 | 0.5144854 | 0.9161150 | 1.0000000 |
| 91 | HOOK2 | 12876937 | 0.2551046 | 0.2769211 | 0.9177988 | 1.0000000 |
| 37 | HLA-DPB1 | 33048370 | 0.7317450 | 0.7210373 | 0.9266991 | 1.0000000 |
| 82 | HOOK2 | 12877020 | 0.2464723 | 0.2684078 | 0.9396705 | 1.0000000 |
| 90 | HOOK2 | 12876942 | 0.2636881 | 0.2861320 | 0.9396705 | 1.0000000 |
| 92 | HOOK2 | 12876926 | 0.2654917 | 0.2876337 | 0.9506242 | 1.0000000 |
| 109 | GFPT2 | 179740888 | 0.5673834 | 0.5590831 | 0.9506242 | 1.0000000 |
| 112 | GFPT2 | 179740861 | 0.6917503 | 0.6963664 | 0.9506242 | 1.0000000 |
| 113 | GFPT2 | 179740855 | 0.7143285 | 0.7204086 | 0.9506242 | 1.0000000 |
| 117 | GFPT2 | 179740825 | 0.7096671 | 0.7123661 | 0.9725570 | 1.0000000 |
| 33 | COX7A2 | 75953974 | 0.2466861 | 0.2413041 | 0.9823349 | 1.0000000 |
| 110 | GFPT2 | 179740869 | 0.6744261 | 0.6738677 | 0.9835322 | 1.0000000 |
| 111 | GFPT2 | 179740867 | 0.6619451 | 0.6670694 | 0.9835322 | 1.0000000 |
| 114 | GFPT2 | 179740852 | 0.6748221 | 0.6786374 | 0.9835322 | 1.0000000 |
| 137 | HLA-DPB1 | 33048549 | 0.9239807 | 0.9253918 | 0.9942798 | 1.0000000 |
| 115 | GFPT2 | 179740840 | 0.6925568 | 0.6979930 | 0.9945104 | 1.0000000 |
| 53 | HOOK2 | 12877107 | 0.2575799 | 0.2701639 | 1.0000000 | 1.0000000 |
3.3.3.2 Figure14: The Differential methylated CpGsites between dcSSc lcSSc patients and Controls
[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD4+ T cells is 9"
[1] "Plot the figure of IFITM1 313408"
[1] "Plot the figure of MX1 42798829"
[1] "Plot the figure of MX1 42798695"
[1] "Plot the figure of MX1 42798863"
[1] "Plot the figure of MX1 42798857"
[1] "Plot the figure of MX1 42798816"
[1] "Plot the figure of FAM132A 1178105"
[1] "Plot the figure of MX1 42798698"
[1] "Plot the figure of MX1 42798749"
3.3.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
3.3.4.1 Table 17: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
| Gene | Pos | Mean.CD4.dc | Mean.CD4.lc | P.value.CD4.dc.lc | FDR | |
|---|---|---|---|---|---|---|
| 28 | COX7A2 | 75953821 | 0.0446434 | 0.0740679 | 0.0012448 | 0.1916966 |
| 65 | COX7A2 | 75954022 | 0.4518312 | 0.5760375 | 0.0031203 | 0.2402595 |
| 51 | IFITM1 | 313408 | 0.2193774 | 0.1796731 | 0.0060829 | 0.2782194 |
| 8 | MX1 | 42798813 | 0.1528304 | 0.1135797 | 0.0122522 | 0.2782194 |
| 30 | COX7A2 | 75953883 | 0.1399584 | 0.1982248 | 0.0122754 | 0.2782194 |
| 31 | COX7A2 | 75953937 | 0.0805141 | 0.1164504 | 0.0133774 | 0.2782194 |
| 32 | COX7A2 | 75953960 | 0.1555675 | 0.2193472 | 0.0133774 | 0.2782194 |
| 1 | MX1 | 42798695 | 0.0381601 | 0.0310149 | 0.0144530 | 0.2782194 |
| 125 | FAM132A | 1178150 | 0.9220973 | 0.9134462 | 0.0183862 | 0.2835113 |
| 66 | COX7A2 | 75954118 | 0.4110438 | 0.4965062 | 0.0198853 | 0.2835113 |
| 29 | COX7A2 | 75953829 | 0.1264856 | 0.1864159 | 0.0202508 | 0.2835113 |
| 9 | MX1 | 42798816 | 0.1525878 | 0.1156618 | 0.0290299 | 0.3725503 |
| 67 | COX7A2 | 75954122 | 0.3666147 | 0.4539439 | 0.0335651 | 0.3837527 |
| 11 | MX1 | 42798829 | 0.1365556 | 0.1036581 | 0.0360453 | 0.3837527 |
| 33 | COX7A2 | 75953974 | 0.1823139 | 0.2466861 | 0.0373785 | 0.3837527 |
| 10 | MX1 | 42798818 | 0.0941620 | 0.0722424 | 0.0475350 | 0.4326570 |
| 12 | MX1 | 42798837 | 0.0850276 | 0.0678139 | 0.0579914 | 0.4326570 |
| 14 | MX1 | 42798857 | 0.1718197 | 0.1361146 | 0.0579914 | 0.4326570 |
| 15 | MX1 | 42798863 | 0.1933493 | 0.1501772 | 0.0618647 | 0.4326570 |
| 21 | RNF39 | 30039186 | 0.1254795 | 0.1517492 | 0.0659440 | 0.4326570 |
| 136 | HLA-DPB1 | 33048544 | 0.8773159 | 0.9462467 | 0.0659440 | 0.4326570 |
| 2 | MX1 | 42798698 | 0.0308387 | 0.0264856 | 0.0702365 | 0.4326570 |
| 6 | MX1 | 42798765 | 0.0317686 | 0.0271204 | 0.0702365 | 0.4326570 |
| 37 | HLA-DPB1 | 33048370 | 0.6273491 | 0.7317450 | 0.0702365 | 0.4326570 |
| 135 | HLA-DPB1 | 33048542 | 0.0683155 | 0.0516326 | 0.0702365 | 0.4326570 |
| 7 | MX1 | 42798781 | 0.0723267 | 0.0609176 | 0.0794904 | 0.4708280 |
| 25 | RNF39 | 30039232 | 0.1782205 | 0.2117913 | 0.0844242 | 0.4815304 |
| 139 | HLA-DPB1 | 33048575 | 0.8728620 | 0.9404808 | 0.0896849 | 0.4932672 |
| 5 | MX1 | 42798749 | 0.0309253 | 0.0271947 | 0.1008781 | 0.5011366 |
| 13 | MX1 | 42798847 | 0.1465303 | 0.1160429 | 0.1008781 | 0.5011366 |
| 141 | HLA-DPB1 | 33048592 | 0.8785906 | 0.9471922 | 0.1008781 | 0.5011366 |
| 23 | RNF39 | 30039206 | 0.1187244 | 0.1472846 | 0.1068671 | 0.5142981 |
| 151 | UPK3B | 76145628 | 0.7062744 | 0.7342650 | 0.1131272 | 0.5279269 |
| 133 | HLA-DPB1 | 33048433 | 0.8554437 | 0.9256979 | 0.1324012 | 0.5869205 |
| 59 | BRDT | 92414650 | 0.4258523 | 0.3824652 | 0.1336017 | 0.5869205 |
| 145 | IFITM1 | 312434 | 0.2057482 | 0.1337707 | 0.1395435 | 0.5869205 |
| 138 | HLA-DPB1 | 33048571 | 0.8724026 | 0.9391389 | 0.1410134 | 0.5869205 |
| 128 | FAM132A | 1178105 | 0.9789670 | 0.9768675 | 0.1632381 | 0.6525123 |
| 20 | RNF39 | 30039158 | 0.1019108 | 0.1247689 | 0.1737588 | 0.6525123 |
| 146 | IFITM1 | 312463 | 0.1562166 | 0.1053054 | 0.1775117 | 0.6525123 |
| 24 | RNF39 | 30039208 | 0.1471008 | 0.1726732 | 0.1827480 | 0.6525123 |
| 131 | HLA-DPB1 | 33048417 | 0.8528855 | 0.9171898 | 0.1827480 | 0.6525123 |
| 132 | HLA-DPB1 | 33048423 | 0.8696502 | 0.9347152 | 0.1827480 | 0.6525123 |
| 22 | RNF39 | 30039202 | 0.1501742 | 0.1729478 | 0.1944141 | 0.6525123 |
| 152 | UPK3B | 76145620 | 0.7966523 | 0.8118123 | 0.2140627 | 0.6525123 |
| 144 | IFITM1 | 312419 | 0.0729589 | 0.0619931 | 0.2220012 | 0.6525123 |
| 142 | HLA-DPB1 | 33048602 | 0.4494760 | 0.6051056 | 0.2220643 | 0.6525123 |
| 18 | RNF39 | 30039130 | 0.1422862 | 0.1686253 | 0.2327535 | 0.6525123 |
| 112 | GFPT2 | 179740861 | 0.7560015 | 0.6917503 | 0.2327535 | 0.6525123 |
| 113 | GFPT2 | 179740855 | 0.7807848 | 0.7143285 | 0.2327535 | 0.6525123 |
| 17 | RNF39 | 30039127 | 0.3078670 | 0.3420550 | 0.2437936 | 0.6525123 |
| 52 | HOOK2 | 12877099 | 0.2306115 | 0.2565141 | 0.2437936 | 0.6525123 |
| 63 | BRDT | 92414770 | 0.7509697 | 0.7249593 | 0.2437936 | 0.6525123 |
| 118 | GFPT2 | 179740822 | 0.7419350 | 0.6747754 | 0.2437936 | 0.6525123 |
| 3 | MX1 | 42798723 | 0.0513214 | 0.0468764 | 0.2551874 | 0.6525123 |
| 16 | RNF39 | 30039123 | 0.3614561 | 0.3909412 | 0.2551874 | 0.6525123 |
| 116 | GFPT2 | 179740832 | 0.7763586 | 0.7093739 | 0.2551874 | 0.6525123 |
| 64 | BRDT | 92414793 | 0.8320961 | 0.8058962 | 0.2634937 | 0.6525123 |
| 26 | RNF39 | 30039235 | 0.1358569 | 0.1583816 | 0.2669368 | 0.6525123 |
| 42 | RNF39 | 30039307 | 0.1733708 | 0.1928048 | 0.2669368 | 0.6525123 |
| 114 | GFPT2 | 179740852 | 0.7368690 | 0.6748221 | 0.2669368 | 0.6525123 |
| 117 | GFPT2 | 179740825 | 0.7798747 | 0.7096671 | 0.2669368 | 0.6525123 |
| 130 | BRDT | 92418017 | 0.9728535 | 0.9699854 | 0.2669368 | 0.6525123 |
| 115 | GFPT2 | 179740840 | 0.7598012 | 0.6925568 | 0.2915099 | 0.7014458 |
| 110 | GFPT2 | 179740869 | 0.7353703 | 0.6744261 | 0.3175214 | 0.7522814 |
| 81 | TLR1 | 38805839 | 0.0596818 | 0.0494588 | 0.3267934 | 0.7625179 |
| 4 | MX1 | 42798733 | 0.0346634 | 0.0322124 | 0.3449715 | 0.7903144 |
| 40 | RNF39 | 30039278 | 0.3409712 | 0.3656945 | 0.3592338 | 0.7903144 |
| 54 | HOOK2 | 12877138 | 0.2542766 | 0.2809405 | 0.3592338 | 0.7903144 |
| 123 | FAM132A | 1178172 | 0.8628519 | 0.8654238 | 0.3592338 | 0.7903144 |
| 19 | RNF39 | 30039132 | 0.0922963 | 0.1037569 | 0.3738520 | 0.7996280 |
| 137 | HLA-DPB1 | 33048549 | 0.8561483 | 0.9239807 | 0.3738520 | 0.7996280 |
| 134 | HLA-DPB1 | 33048444 | 0.8251486 | 0.8968022 | 0.3888238 | 0.8091738 |
| 140 | HLA-DPB1 | 33048581 | 0.8656858 | 0.9277086 | 0.3888238 | 0.8091738 |
| 38 | RNF39 | 30039271 | 0.1879945 | 0.2014079 | 0.4041460 | 0.8163565 |
| 53 | HOOK2 | 12877107 | 0.2337943 | 0.2575799 | 0.4041460 | 0.8163565 |
| 68 | HELZ2 | 62199061 | 0.0356405 | 0.0448612 | 0.4081783 | 0.8163565 |
| 80 | EIF2AK2 | 37383730 | 0.0263226 | 0.0247515 | 0.4319174 | 0.8389670 |
| 62 | BRDT | 92414751 | 0.7326712 | 0.7109765 | 0.4358270 | 0.8389670 |
| 120 | FAM132A | 1178202 | 0.7827009 | 0.7802450 | 0.4358270 | 0.8389670 |
| 126 | FAM132A | 1178136 | 0.9701882 | 0.9714783 | 0.4521770 | 0.8441006 |
| 47 | RNF39 | 30039364 | 0.1044725 | 0.1073149 | 0.4688597 | 0.8441006 |
| 58 | HOOK2 | 12877276 | 0.2590516 | 0.2859800 | 0.4688597 | 0.8441006 |
| 94 | HOOK2 | 12876911 | 0.2628716 | 0.2962037 | 0.4858693 | 0.8441006 |
| 98 | GFPT2 | 179740992 | 0.6312012 | 0.5793734 | 0.4858693 | 0.8441006 |
| 50 | RNF39 | 30039418 | 0.4442470 | 0.4656233 | 0.5031992 | 0.8441006 |
| 82 | HOOK2 | 12877020 | 0.2123525 | 0.2464723 | 0.5031992 | 0.8441006 |
| 92 | HOOK2 | 12876926 | 0.2325951 | 0.2654917 | 0.5031992 | 0.8441006 |
| 97 | GFPT2 | 179740994 | 0.6448891 | 0.5932223 | 0.5031992 | 0.8441006 |
| 104 | GFPT2 | 179740935 | 0.6806278 | 0.6228022 | 0.5031992 | 0.8441006 |
| 43 | RNF39 | 30039313 | 0.2053626 | 0.2208833 | 0.5208424 | 0.8441006 |
| 44 | RNF39 | 30039323 | 0.2670671 | 0.2895114 | 0.5344638 | 0.8441006 |
| 71 | GFPT2 | 179741067 | 0.5638664 | 0.5212852 | 0.5387912 | 0.8441006 |
| 111 | GFPT2 | 179740867 | 0.7217714 | 0.6619451 | 0.5387912 | 0.8441006 |
| 153 | UPK3B | 76145606 | 0.3782685 | 0.3904465 | 0.5387912 | 0.8441006 |
| 154 | UPK3B | 76145589 | 0.1720512 | 0.1765031 | 0.5387912 | 0.8441006 |
| 35 | SMAD3 | 67361821 | 0.8864407 | 0.8999875 | 0.5527815 | 0.8441006 |
| 49 | RNF39 | 30039415 | 0.2266577 | 0.2420830 | 0.5570375 | 0.8441006 |
| 96 | GFPT2 | 179740999 | 0.6234426 | 0.5743277 | 0.5570375 | 0.8441006 |
| 102 | GFPT2 | 179740955 | 0.6733490 | 0.6193809 | 0.5570375 | 0.8441006 |
| 46 | RNF39 | 30039354 | 0.2246827 | 0.2356277 | 0.5714019 | 0.8441006 |
| 48 | RNF39 | 30039411 | 0.4167763 | 0.4355559 | 0.5755724 | 0.8441006 |
| 85 | HOOK2 | 12876987 | 0.2186697 | 0.2531426 | 0.5755724 | 0.8441006 |
| 109 | GFPT2 | 179740888 | 0.6252246 | 0.5673834 | 0.5755724 | 0.8441006 |
| 100 | GFPT2 | 179740963 | 0.6543772 | 0.6027175 | 0.5943868 | 0.8441006 |
| 124 | FAM132A | 1178162 | 0.8130103 | 0.8095996 | 0.5943868 | 0.8441006 |
| 76 | EIF2AK2 | 37383588 | 0.0759636 | 0.0681276 | 0.5975265 | 0.8441006 |
| 36 | SMAD3 | 67361896 | 0.8435264 | 0.8366558 | 0.6134706 | 0.8441006 |
| 61 | BRDT | 92414719 | 0.3078300 | 0.2966023 | 0.6134706 | 0.8441006 |
| 95 | GFPT2 | 179741008 | 0.5565324 | 0.5100013 | 0.6134706 | 0.8441006 |
| 101 | GFPT2 | 179740957 | 0.6711285 | 0.6170463 | 0.6134706 | 0.8441006 |
| 74 | GFPT2 | 179741042 | 0.4692564 | 0.4257726 | 0.6328136 | 0.8441006 |
| 91 | HOOK2 | 12876937 | 0.2229114 | 0.2551046 | 0.6328136 | 0.8441006 |
| 93 | HOOK2 | 12876918 | 0.2439106 | 0.2763449 | 0.6328136 | 0.8441006 |
| 107 | GFPT2 | 179740906 | 0.6711654 | 0.6141981 | 0.6328136 | 0.8441006 |
| 148 | UPK3B | 76145702 | 0.2841578 | 0.2946057 | 0.6486972 | 0.8441006 |
| 41 | RNF39 | 30039303 | 0.1915649 | 0.2016737 | 0.6524049 | 0.8441006 |
| 75 | GFPT2 | 179741039 | 0.6135393 | 0.5627541 | 0.6524049 | 0.8441006 |
| 108 | GFPT2 | 179740900 | 0.6263760 | 0.5783244 | 0.6524049 | 0.8441006 |
| 27 | RNF39 | 30039239 | 0.3243063 | 0.3358206 | 0.6722331 | 0.8441006 |
| 103 | GFPT2 | 179740940 | 0.6335832 | 0.5797049 | 0.6722331 | 0.8441006 |
| 106 | GFPT2 | 179740918 | 0.6526585 | 0.5980296 | 0.6722331 | 0.8441006 |
| 79 | EIF2AK2 | 37383713 | 0.0083365 | 0.0112373 | 0.6791509 | 0.8441006 |
| 70 | GFPT2 | 179741081 | 0.5870507 | 0.5497762 | 0.6922864 | 0.8441006 |
| 105 | GFPT2 | 179740920 | 0.6286866 | 0.5778832 | 0.6922864 | 0.8441006 |
| 119 | FAM132A | 1178207 | 0.8479868 | 0.8456628 | 0.6922864 | 0.8441006 |
| 39 | RNF39 | 30039274 | 0.2086611 | 0.2208201 | 0.7125525 | 0.8441006 |
| 60 | BRDT | 92414661 | 0.5263980 | 0.5161855 | 0.7125525 | 0.8441006 |
| 72 | GFPT2 | 179741063 | 0.5645206 | 0.5215559 | 0.7125525 | 0.8441006 |
| 99 | GFPT2 | 179740970 | 0.5854953 | 0.5409305 | 0.7125525 | 0.8441006 |
| 73 | GFPT2 | 179741060 | 0.6235241 | 0.5755289 | 0.7330186 | 0.8487584 |
| 87 | HOOK2 | 12876948 | 0.2287765 | 0.2619367 | 0.7330186 | 0.8487584 |
| 90 | HOOK2 | 12876942 | 0.2300281 | 0.2636881 | 0.7330186 | 0.8487584 |
| 150 | UPK3B | 76145689 | 0.3570678 | 0.3532317 | 0.7404102 | 0.8509192 |
| 77 | EIF2AK2 | 37383623 | 0.0132245 | 0.0142002 | 0.7617952 | 0.8690108 |
| 57 | HOOK2 | 12877235 | 0.3206069 | 0.3413112 | 0.7744984 | 0.8770056 |
| 143 | IFI44L | 79085647 | 0.1195439 | 0.1143348 | 0.7864803 | 0.8840727 |
| 127 | FAM132A | 1178118 | 0.9495490 | 0.9517401 | 0.7954847 | 0.8877148 |
| 78 | EIF2AK2 | 37383679 | 0.0143214 | 0.0167932 | 0.8085050 | 0.8957537 |
| 55 | HOOK2 | 12877201 | 0.2941553 | 0.3168446 | 0.8166164 | 0.8982780 |
| 121 | FAM132A | 1178192 | 0.9283732 | 0.9283924 | 0.8378791 | 0.9151304 |
| 56 | HOOK2 | 12877215 | 0.2709562 | 0.2927520 | 0.8592579 | 0.9189286 |
| 69 | GFPT2 | 179741101 | 0.5996110 | 0.5579517 | 0.8592579 | 0.9189286 |
| 89 | HOOK2 | 12876944 | 0.2283631 | 0.2607402 | 0.8592579 | 0.9189286 |
| 88 | HOOK2 | 12876946 | 0.2254400 | 0.2591300 | 0.8807380 | 0.9354045 |
| 122 | FAM132A | 1178182 | 0.7929911 | 0.7943505 | 0.9023041 | 0.9452709 |
| 149 | UPK3B | 76145693 | 0.5311877 | 0.5291985 | 0.9023041 | 0.9452709 |
| 45 | RNF39 | 30039349 | 0.1943104 | 0.2053414 | 0.9120630 | 0.9490386 |
| 83 | HOOK2 | 12876997 | 0.2060073 | 0.2361947 | 0.9456325 | 0.9708494 |
| 84 | HOOK2 | 12876993 | 0.2152394 | 0.2462851 | 0.9456325 | 0.9708494 |
| 86 | HOOK2 | 12876969 | 0.2234150 | 0.2551195 | 0.9891186 | 0.9955834 |
| 129 | FAM132A | 1178086 | 0.9193654 | 0.9182644 | 0.9891186 | 0.9955834 |
| 147 | UPK3B | 76145717 | 0.4323066 | 0.4356264 | 0.9891186 | 0.9955834 |
| 34 | SMAD3 | 67361798 | 0.9058747 | 0.9061659 | 1.0000000 | 1.0000000 |
3.3.4.2 Figure15: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 15 in our analysis."
3.4 Validation of differential methylated CpGsites only in the validation stage due to the sequencing advantage in CD8+
3.4.1 Validation of differential methylated CpGsites between SSc patients and Controls
3.4.1.1 Table 18: The Differential methylated CpGsites between SSc patients and Controls
| Gene | Pos | Mean.CD8.SSc | Mean.CD8.NC | P.value.CD8.SSC.NC | FDR | |
|---|---|---|---|---|---|---|
| 15 | MX1 | 42798863 | 0.2158335 | 0.2972670 | 0.0001326 | 0.0088424 |
| 12 | MX1 | 42798837 | 0.1068262 | 0.1505124 | 0.0001555 | 0.0088424 |
| 14 | MX1 | 42798857 | 0.1851206 | 0.2552752 | 0.0001820 | 0.0088424 |
| 9 | MX1 | 42798816 | 0.1682997 | 0.2208034 | 0.0002297 | 0.0088424 |
| 11 | MX1 | 42798829 | 0.1646297 | 0.2197405 | 0.0003753 | 0.0115607 |
| 13 | MX1 | 42798847 | 0.1897550 | 0.2580407 | 0.0007640 | 0.0170880 |
| 8 | MX1 | 42798813 | 0.1796408 | 0.2377021 | 0.0007767 | 0.0170880 |
| 10 | MX1 | 42798818 | 0.1205289 | 0.1598394 | 0.0009838 | 0.0189387 |
| 7 | MX1 | 42798781 | 0.1046483 | 0.1345820 | 0.0012065 | 0.0206453 |
| 4 | MX1 | 42798733 | 0.0403381 | 0.0506473 | 0.0028125 | 0.0433129 |
| 78 | EIF2AK2 | 37383679 | 0.0122648 | 0.0161317 | 0.0054003 | 0.0756042 |
| 50 | RNF39 | 30039418 | 0.4389772 | 0.5283172 | 0.0063838 | 0.0819258 |
| 80 | EIF2AK2 | 37383730 | 0.0248620 | 0.0340524 | 0.0095065 | 0.1126158 |
| 5 | MX1 | 42798749 | 0.0357276 | 0.0423275 | 0.0125292 | 0.1378210 |
| 6 | MX1 | 42798765 | 0.0408280 | 0.0470983 | 0.0176582 | 0.1812907 |
| 76 | EIF2AK2 | 37383588 | 0.0946465 | 0.1141754 | 0.0206115 | 0.1983858 |
| 143 | IFI44L | 79085647 | 0.1689546 | 0.2059993 | 0.0238435 | 0.2159944 |
| 3 | MX1 | 42798723 | 0.0614809 | 0.0700709 | 0.0286238 | 0.2448928 |
| 131 | HLA-DPB1 | 33048417 | 0.9098175 | 0.9399218 | 0.0424526 | 0.3313670 |
| 48 | RNF39 | 30039411 | 0.4391145 | 0.5018491 | 0.0441026 | 0.3313670 |
| 45 | RNF39 | 30039349 | 0.2378623 | 0.3019271 | 0.0451864 | 0.3313670 |
| 141 | HLA-DPB1 | 33048592 | 0.9288820 | 0.9615786 | 0.0495997 | 0.3380849 |
| 40 | RNF39 | 30039278 | 0.3795850 | 0.4356661 | 0.0504932 | 0.3380849 |
| 44 | RNF39 | 30039323 | 0.2883827 | 0.3438164 | 0.0560013 | 0.3593416 |
| 144 | IFITM1 | 312419 | 0.0739377 | 0.1019998 | 0.0601917 | 0.3707811 |
| 139 | HLA-DPB1 | 33048575 | 0.9252925 | 0.9567140 | 0.0768833 | 0.4398828 |
| 125 | FAM132A | 1178150 | 0.9022968 | 0.9091035 | 0.0771223 | 0.4398828 |
| 46 | RNF39 | 30039354 | 0.2404657 | 0.3102584 | 0.0827823 | 0.4553024 |
| 42 | RNF39 | 30039307 | 0.1729444 | 0.2349002 | 0.0895704 | 0.4631989 |
| 41 | RNF39 | 30039303 | 0.2101137 | 0.2680066 | 0.0931316 | 0.4631989 |
| 77 | EIF2AK2 | 37383623 | 0.0150487 | 0.0172126 | 0.0932413 | 0.4631989 |
| 134 | HLA-DPB1 | 33048444 | 0.8794711 | 0.9096903 | 0.1006822 | 0.4845333 |
| 52 | HOOK2 | 12877099 | 0.2279291 | 0.2514190 | 0.1055379 | 0.4925104 |
| 49 | RNF39 | 30039415 | 0.2846470 | 0.3286858 | 0.1202159 | 0.5437163 |
| 43 | RNF39 | 30039313 | 0.2371394 | 0.2898949 | 0.1235719 | 0.5437163 |
| 137 | HLA-DPB1 | 33048549 | 0.9094355 | 0.9341162 | 0.1300042 | 0.5561291 |
| 51 | IFITM1 | 313408 | 0.1764488 | 0.1866750 | 0.1370834 | 0.5705634 |
| 138 | HLA-DPB1 | 33048571 | 0.9164888 | 0.9467651 | 0.1420384 | 0.5756292 |
| 136 | HLA-DPB1 | 33048544 | 0.9300397 | 0.9584988 | 0.1461612 | 0.5771493 |
| 149 | UPK3B | 76145693 | 0.5685306 | 0.5530011 | 0.1517809 | 0.5843565 |
| 53 | HOOK2 | 12877107 | 0.2314636 | 0.2541165 | 0.1804528 | 0.6658105 |
| 154 | UPK3B | 76145589 | 0.2019851 | 0.1890741 | 0.1815847 | 0.6658105 |
| 2 | MX1 | 42798698 | 0.0415546 | 0.0458381 | 0.1860967 | 0.6664858 |
| 39 | RNF39 | 30039274 | 0.2247512 | 0.2734733 | 0.1924404 | 0.6735413 |
| 151 | UPK3B | 76145628 | 0.7344427 | 0.7505882 | 0.2037455 | 0.6972625 |
| 1 | MX1 | 42798695 | 0.0466905 | 0.0489980 | 0.2171385 | 0.7131396 |
| 150 | UPK3B | 76145689 | 0.4062791 | 0.3921679 | 0.2207433 | 0.7131396 |
| 146 | IFITM1 | 312463 | 0.1395583 | 0.1586609 | 0.2222773 | 0.7131396 |
| 145 | IFITM1 | 312434 | 0.1774891 | 0.1993537 | 0.2406777 | 0.7564156 |
| 47 | RNF39 | 30039364 | 0.1515930 | 0.1401614 | 0.2495756 | 0.7686928 |
| 140 | HLA-DPB1 | 33048581 | 0.9098786 | 0.9389990 | 0.2598686 | 0.7847012 |
| 128 | FAM132A | 1178105 | 0.9783984 | 0.9761999 | 0.2732366 | 0.8092007 |
| 68 | HELZ2 | 62199061 | 0.0407535 | 0.0335129 | 0.2794895 | 0.8121017 |
| 133 | HLA-DPB1 | 33048433 | 0.9232463 | 0.9465281 | 0.2959848 | 0.8441048 |
| 38 | RNF39 | 30039271 | 0.2242318 | 0.2627923 | 0.3186390 | 0.8921893 |
| 69 | GFPT2 | 179741101 | 0.5799309 | 0.5436586 | 0.3482935 | 0.9260539 |
| 105 | GFPT2 | 179740920 | 0.5882954 | 0.5588129 | 0.3523922 | 0.9260539 |
| 54 | HOOK2 | 12877138 | 0.2638735 | 0.2828210 | 0.3824304 | 0.9260539 |
| 25 | RNF39 | 30039232 | 0.2572461 | 0.2765787 | 0.4031654 | 0.9260539 |
| 100 | GFPT2 | 179740963 | 0.6021399 | 0.5755657 | 0.4117597 | 0.9260539 |
| 103 | GFPT2 | 179740940 | 0.5820856 | 0.5537678 | 0.4169584 | 0.9260539 |
| 58 | HOOK2 | 12877276 | 0.2465499 | 0.2671606 | 0.4174312 | 0.9260539 |
| 94 | HOOK2 | 12876911 | 0.2798731 | 0.3049543 | 0.4277642 | 0.9260539 |
| 34 | SMAD3 | 67361798 | 0.9372159 | 0.9274174 | 0.4290607 | 0.9260539 |
| 99 | GFPT2 | 179740970 | 0.5475317 | 0.5222309 | 0.4381325 | 0.9260539 |
| 108 | GFPT2 | 179740900 | 0.5866370 | 0.5621152 | 0.4435200 | 0.9260539 |
| 142 | HLA-DPB1 | 33048602 | 0.5233596 | 0.5938896 | 0.4444654 | 0.9260539 |
| 107 | GFPT2 | 179740906 | 0.6251411 | 0.5964526 | 0.4489448 | 0.9260539 |
| 37 | HLA-DPB1 | 33048370 | 0.7327415 | 0.7459280 | 0.4544065 | 0.9260539 |
| 123 | FAM132A | 1178172 | 0.8245171 | 0.8278377 | 0.4628546 | 0.9260539 |
| 97 | GFPT2 | 179740994 | 0.5941014 | 0.5692321 | 0.4766200 | 0.9260539 |
| 98 | GFPT2 | 179740992 | 0.5831624 | 0.5598780 | 0.4822639 | 0.9260539 |
| 35 | SMAD3 | 67361821 | 0.9348617 | 0.9361443 | 0.4828773 | 0.9260539 |
| 17 | RNF39 | 30039127 | 0.3841659 | 0.3731225 | 0.4836774 | 0.9260539 |
| 62 | BRDT | 92414751 | 0.5075202 | 0.4788894 | 0.4857102 | 0.9260539 |
| 101 | GFPT2 | 179740957 | 0.6177339 | 0.5937250 | 0.4879435 | 0.9260539 |
| 114 | GFPT2 | 179740852 | 0.6846808 | 0.6570538 | 0.4994089 | 0.9260539 |
| 36 | SMAD3 | 67361896 | 0.8997473 | 0.8938339 | 0.5025998 | 0.9260539 |
| 72 | GFPT2 | 179741063 | 0.5353806 | 0.5105164 | 0.5032403 | 0.9260539 |
| 57 | HOOK2 | 12877235 | 0.3506097 | 0.3714093 | 0.5040958 | 0.9260539 |
| 64 | BRDT | 92414793 | 0.5672853 | 0.5366430 | 0.5041728 | 0.9260539 |
| 102 | GFPT2 | 179740955 | 0.6219072 | 0.5986114 | 0.5051942 | 0.9260539 |
| 106 | GFPT2 | 179740918 | 0.6050829 | 0.5829248 | 0.5051942 | 0.9260539 |
| 111 | GFPT2 | 179740867 | 0.6819934 | 0.6576121 | 0.5110143 | 0.9260539 |
| 126 | FAM132A | 1178136 | 0.9680554 | 0.9694773 | 0.5271179 | 0.9260539 |
| 95 | GFPT2 | 179741008 | 0.5057461 | 0.4843944 | 0.5346363 | 0.9260539 |
| 96 | GFPT2 | 179740999 | 0.5800966 | 0.5572977 | 0.5346363 | 0.9260539 |
| 104 | GFPT2 | 179740935 | 0.6247533 | 0.5997596 | 0.5346363 | 0.9260539 |
| 109 | GFPT2 | 179740888 | 0.5908451 | 0.5645584 | 0.5406258 | 0.9260539 |
| 31 | COX7A2 | 75953937 | 0.1267371 | 0.1354768 | 0.5624329 | 0.9260539 |
| 19 | RNF39 | 30039132 | 0.1526993 | 0.1601234 | 0.5683198 | 0.9260539 |
| 24 | RNF39 | 30039208 | 0.2103395 | 0.2166896 | 0.5683219 | 0.9260539 |
| 33 | COX7A2 | 75953974 | 0.2455319 | 0.2586032 | 0.5754383 | 0.9260539 |
| 71 | GFPT2 | 179741067 | 0.5420300 | 0.5217057 | 0.5892100 | 0.9260539 |
| 110 | GFPT2 | 179740869 | 0.6871845 | 0.6635659 | 0.5897022 | 0.9260539 |
| 70 | GFPT2 | 179741081 | 0.5641737 | 0.5435904 | 0.5955982 | 0.9260539 |
| 55 | HOOK2 | 12877201 | 0.3218085 | 0.3389160 | 0.5993194 | 0.9260539 |
| 28 | COX7A2 | 75953821 | 0.0779455 | 0.0821239 | 0.6085513 | 0.9260539 |
| 30 | COX7A2 | 75953883 | 0.1954050 | 0.2034265 | 0.6085513 | 0.9260539 |
| 152 | UPK3B | 76145620 | 0.8167159 | 0.8091339 | 0.6131467 | 0.9260539 |
| 112 | GFPT2 | 179740861 | 0.7060889 | 0.6855562 | 0.6149784 | 0.9260539 |
| 67 | COX7A2 | 75954122 | 0.4428005 | 0.4490352 | 0.6262348 | 0.9260539 |
| 74 | GFPT2 | 179741042 | 0.4511989 | 0.4307610 | 0.6279970 | 0.9260539 |
| 115 | GFPT2 | 179740840 | 0.7044013 | 0.6829977 | 0.6342391 | 0.9260539 |
| 63 | BRDT | 92414770 | 0.5137695 | 0.4928876 | 0.6427615 | 0.9260539 |
| 23 | RNF39 | 30039206 | 0.2018929 | 0.2108971 | 0.6561120 | 0.9260539 |
| 113 | GFPT2 | 179740855 | 0.7230183 | 0.7038407 | 0.6603041 | 0.9260539 |
| 73 | GFPT2 | 179741060 | 0.5978390 | 0.5746584 | 0.6611208 | 0.9260539 |
| 118 | GFPT2 | 179740822 | 0.6833521 | 0.6609020 | 0.6619679 | 0.9260539 |
| 147 | UPK3B | 76145717 | 0.4810049 | 0.4732804 | 0.6628272 | 0.9260539 |
| 32 | COX7A2 | 75953960 | 0.2324648 | 0.2463432 | 0.6701641 | 0.9260539 |
| 116 | GFPT2 | 179740832 | 0.7206030 | 0.6991309 | 0.6734937 | 0.9260539 |
| 130 | BRDT | 92418017 | 0.9733938 | 0.9726775 | 0.6818992 | 0.9293139 |
| 132 | HLA-DPB1 | 33048423 | 0.9307672 | 0.9505762 | 0.6908851 | 0.9333009 |
| 26 | RNF39 | 30039235 | 0.2392387 | 0.2488515 | 0.7086060 | 0.9398467 |
| 75 | GFPT2 | 179741039 | 0.5938789 | 0.5738683 | 0.7086060 | 0.9398467 |
| 18 | RNF39 | 30039130 | 0.2194435 | 0.2308035 | 0.7140394 | 0.9398467 |
| 60 | BRDT | 92414661 | 0.4234587 | 0.4071912 | 0.7279296 | 0.9459377 |
| 117 | GFPT2 | 179740825 | 0.7180035 | 0.6970619 | 0.7340324 | 0.9459377 |
| 91 | HOOK2 | 12876937 | 0.2342092 | 0.2565081 | 0.7418712 | 0.9459377 |
| 22 | RNF39 | 30039202 | 0.2375842 | 0.2456934 | 0.7432367 | 0.9459377 |
| 83 | HOOK2 | 12876997 | 0.2163085 | 0.2362756 | 0.7553705 | 0.9465025 |
| 129 | FAM132A | 1178086 | 0.9019360 | 0.8976444 | 0.7559727 | 0.9465025 |
| 79 | EIF2AK2 | 37383713 | 0.0083446 | 0.0076138 | 0.7654747 | 0.9506702 |
| 65 | COX7A2 | 75954022 | 0.5304357 | 0.5349920 | 0.7854763 | 0.9677068 |
| 16 | RNF39 | 30039123 | 0.4574247 | 0.4575020 | 0.7925811 | 0.9687102 |
| 93 | HOOK2 | 12876918 | 0.2571966 | 0.2814326 | 0.8100714 | 0.9751801 |
| 135 | HLA-DPB1 | 33048542 | 0.0633443 | 0.0839724 | 0.8105393 | 0.9751801 |
| 84 | HOOK2 | 12876993 | 0.2246503 | 0.2469626 | 0.8308391 | 0.9759680 |
| 86 | HOOK2 | 12876969 | 0.2353652 | 0.2589791 | 0.8308391 | 0.9759680 |
| 124 | FAM132A | 1178162 | 0.7876508 | 0.7817024 | 0.8427612 | 0.9759680 |
| 87 | HOOK2 | 12876948 | 0.2411423 | 0.2624347 | 0.8587098 | 0.9759680 |
| 56 | HOOK2 | 12877215 | 0.2847495 | 0.3040664 | 0.8657062 | 0.9759680 |
| 119 | FAM132A | 1178207 | 0.8009946 | 0.8002057 | 0.8673836 | 0.9759680 |
| 27 | RNF39 | 30039239 | 0.3921812 | 0.3984258 | 0.8710312 | 0.9759680 |
| 81 | TLR1 | 38805839 | 0.0800520 | 0.0654668 | 0.8801208 | 0.9759680 |
| 153 | UPK3B | 76145606 | 0.4177201 | 0.4140856 | 0.8820041 | 0.9759680 |
| 90 | HOOK2 | 12876942 | 0.2448346 | 0.2689455 | 0.8867558 | 0.9759680 |
| 20 | RNF39 | 30039158 | 0.1617914 | 0.1669710 | 0.8893298 | 0.9759680 |
| 29 | COX7A2 | 75953829 | 0.1900842 | 0.1911202 | 0.8896544 | 0.9759680 |
| 66 | COX7A2 | 75954118 | 0.4763134 | 0.4770666 | 0.8935811 | 0.9759680 |
| 82 | HOOK2 | 12877020 | 0.2262234 | 0.2465793 | 0.9078847 | 0.9846073 |
| 148 | UPK3B | 76145702 | 0.3201036 | 0.3185503 | 0.9260873 | 0.9848891 |
| 92 | HOOK2 | 12876926 | 0.2451798 | 0.2694612 | 0.9290783 | 0.9848891 |
| 127 | FAM132A | 1178118 | 0.9413770 | 0.9412087 | 0.9334608 | 0.9848891 |
| 121 | FAM132A | 1178192 | 0.8986722 | 0.8958672 | 0.9374958 | 0.9848891 |
| 89 | HOOK2 | 12876944 | 0.2412735 | 0.2659038 | 0.9503217 | 0.9848891 |
| 122 | FAM132A | 1178182 | 0.7394479 | 0.7345481 | 0.9521825 | 0.9848891 |
| 85 | HOOK2 | 12876987 | 0.2314150 | 0.2545267 | 0.9574114 | 0.9848891 |
| 61 | BRDT | 92414719 | 0.2879416 | 0.2957146 | 0.9593076 | 0.9848891 |
| 120 | FAM132A | 1178202 | 0.7308277 | 0.7274506 | 0.9740981 | 0.9906631 |
| 21 | RNF39 | 30039186 | 0.2308739 | 0.2303945 | 0.9777974 | 0.9906631 |
| 88 | HOOK2 | 12876946 | 0.2385206 | 0.2610126 | 0.9857979 | 0.9922410 |
| 59 | BRDT | 92414650 | 0.3461574 | 0.3381310 | 0.9925983 | 0.9925983 |
3.4.1.2 Figure16: The Differential methylated CpGsites between SSc patients and Controls
[1] "The number of significant differential methylated CpGsites between SSc patients and normal controls in CD8+ T cells is 10"
[1] "Plot the figure of MX1 42798863"
[1] "Plot the figure of MX1 42798837"
[1] "Plot the figure of MX1 42798857"
[1] "Plot the figure of MX1 42798816"
[1] "Plot the figure of MX1 42798829"
[1] "Plot the figure of MX1 42798847"
[1] "Plot the figure of MX1 42798813"
[1] "Plot the figure of MX1 42798818"
[1] "Plot the figure of MX1 42798781"
[1] "Plot the figure of MX1 42798733"
3.4.2 Validation of differential methylated CpGsites between dcSSc patients and Controls
3.4.2.1 Table 19: The Differential methylated CpGsites between dcSSc patients and Controls
| Gene | Pos | Mean.CD8.dc | Mean.CD8.NC | P.value.CD8.dc.NC | FDR | |
|---|---|---|---|---|---|---|
| 151 | UPK3B | 76145628 | 0.7168508 | 0.7505882 | 0.0074676 | 0.6275811 |
| 137 | HLA-DPB1 | 33048549 | 0.8846894 | 0.9341162 | 0.0357128 | 0.6275811 |
| 67 | COX7A2 | 75954122 | 0.3900427 | 0.4490352 | 0.0404422 | 0.6275811 |
| 31 | COX7A2 | 75953937 | 0.1020046 | 0.1354768 | 0.0412963 | 0.6275811 |
| 136 | HLA-DPB1 | 33048544 | 0.9068650 | 0.9584988 | 0.0472206 | 0.6275811 |
| 30 | COX7A2 | 75953883 | 0.1609718 | 0.2034265 | 0.0520467 | 0.6275811 |
| 65 | COX7A2 | 75954022 | 0.4671704 | 0.5349920 | 0.0527722 | 0.6275811 |
| 50 | RNF39 | 30039418 | 0.4424677 | 0.5283172 | 0.0575080 | 0.6275811 |
| 134 | HLA-DPB1 | 33048444 | 0.8559200 | 0.9096903 | 0.0588658 | 0.6275811 |
| 40 | RNF39 | 30039278 | 0.3615585 | 0.4356661 | 0.0600022 | 0.6275811 |
| 28 | COX7A2 | 75953821 | 0.0618621 | 0.0821239 | 0.0622053 | 0.6275811 |
| 37 | HLA-DPB1 | 33048370 | 0.6872302 | 0.7459280 | 0.0630489 | 0.6275811 |
| 133 | HLA-DPB1 | 33048433 | 0.9009518 | 0.9465281 | 0.0678762 | 0.6275811 |
| 66 | COX7A2 | 75954118 | 0.4232681 | 0.4770666 | 0.0738199 | 0.6275811 |
| 15 | MX1 | 42798863 | 0.2567028 | 0.2972670 | 0.0801774 | 0.6275811 |
| 33 | COX7A2 | 75953974 | 0.2048235 | 0.2586032 | 0.0803861 | 0.6275811 |
| 32 | COX7A2 | 75953960 | 0.1962902 | 0.2463432 | 0.0837896 | 0.6275811 |
| 41 | RNF39 | 30039303 | 0.1952517 | 0.2680066 | 0.0866138 | 0.6275811 |
| 141 | HLA-DPB1 | 33048592 | 0.9067151 | 0.9615786 | 0.0870716 | 0.6275811 |
| 14 | MX1 | 42798857 | 0.2210567 | 0.2552752 | 0.1085422 | 0.6275811 |
| 29 | COX7A2 | 75953829 | 0.1553651 | 0.1911202 | 0.1109068 | 0.6275811 |
| 52 | HOOK2 | 12877099 | 0.2162453 | 0.2514190 | 0.1208106 | 0.6275811 |
| 69 | GFPT2 | 179741101 | 0.6244667 | 0.5436586 | 0.1356549 | 0.6275811 |
| 13 | MX1 | 42798847 | 0.2248944 | 0.2580407 | 0.1380952 | 0.6275811 |
| 154 | UPK3B | 76145589 | 0.2005878 | 0.1890741 | 0.1405363 | 0.6275811 |
| 45 | RNF39 | 30039349 | 0.2382702 | 0.3019271 | 0.1506938 | 0.6275811 |
| 128 | FAM132A | 1178105 | 0.9793370 | 0.9761999 | 0.1506938 | 0.6275811 |
| 131 | HLA-DPB1 | 33048417 | 0.8982112 | 0.9399218 | 0.1541931 | 0.6275811 |
| 125 | FAM132A | 1178150 | 0.9015033 | 0.9091035 | 0.1559733 | 0.6275811 |
| 53 | HOOK2 | 12877107 | 0.2193410 | 0.2541165 | 0.1627761 | 0.6275811 |
| 12 | MX1 | 42798837 | 0.1306970 | 0.1505124 | 0.1648895 | 0.6275811 |
| 74 | GFPT2 | 179741042 | 0.5025036 | 0.4307610 | 0.1669421 | 0.6275811 |
| 44 | RNF39 | 30039323 | 0.2900312 | 0.3438164 | 0.1854975 | 0.6275811 |
| 99 | GFPT2 | 179740970 | 0.5887988 | 0.5222309 | 0.1938575 | 0.6275811 |
| 48 | RNF39 | 30039411 | 0.4398426 | 0.5018491 | 0.1946962 | 0.6275811 |
| 11 | MX1 | 42798829 | 0.2007530 | 0.2197405 | 0.2000648 | 0.6275811 |
| 114 | GFPT2 | 179740852 | 0.7266582 | 0.6570538 | 0.2064129 | 0.6275811 |
| 149 | UPK3B | 76145693 | 0.5693504 | 0.5530011 | 0.2097935 | 0.6275811 |
| 105 | GFPT2 | 179740920 | 0.6355716 | 0.5588129 | 0.2129027 | 0.6275811 |
| 71 | GFPT2 | 179741067 | 0.5889373 | 0.5217057 | 0.2164994 | 0.6275811 |
| 107 | GFPT2 | 179740906 | 0.6717459 | 0.5964526 | 0.2195354 | 0.6275811 |
| 108 | GFPT2 | 179740900 | 0.6291681 | 0.5621152 | 0.2195354 | 0.6275811 |
| 102 | GFPT2 | 179740955 | 0.6632321 | 0.5986114 | 0.2263120 | 0.6275811 |
| 109 | GFPT2 | 179740888 | 0.6393397 | 0.5645584 | 0.2263120 | 0.6275811 |
| 70 | GFPT2 | 179741081 | 0.6102137 | 0.5435904 | 0.2303608 | 0.6275811 |
| 72 | GFPT2 | 179741063 | 0.5838811 | 0.5105164 | 0.2303608 | 0.6275811 |
| 46 | RNF39 | 30039354 | 0.2384689 | 0.3102584 | 0.2312846 | 0.6275811 |
| 100 | GFPT2 | 179740963 | 0.6408295 | 0.5755657 | 0.2332332 | 0.6275811 |
| 103 | GFPT2 | 179740940 | 0.6219964 | 0.5537678 | 0.2332332 | 0.6275811 |
| 112 | GFPT2 | 179740861 | 0.7475890 | 0.6855562 | 0.2332332 | 0.6275811 |
| 9 | MX1 | 42798816 | 0.2059071 | 0.2208034 | 0.2475131 | 0.6275811 |
| 8 | MX1 | 42798813 | 0.2192756 | 0.2377021 | 0.2548731 | 0.6275811 |
| 104 | GFPT2 | 179740935 | 0.6658861 | 0.5997596 | 0.2548731 | 0.6275811 |
| 106 | GFPT2 | 179740918 | 0.6521347 | 0.5829248 | 0.2548731 | 0.6275811 |
| 116 | GFPT2 | 179740832 | 0.7624362 | 0.6991309 | 0.2548731 | 0.6275811 |
| 75 | GFPT2 | 179741039 | 0.6485978 | 0.5738683 | 0.2599069 | 0.6275811 |
| 97 | GFPT2 | 179740994 | 0.6334668 | 0.5692321 | 0.2623807 | 0.6275811 |
| 101 | GFPT2 | 179740957 | 0.6589853 | 0.5937250 | 0.2623807 | 0.6275811 |
| 110 | GFPT2 | 179740869 | 0.7297972 | 0.6635659 | 0.2623807 | 0.6275811 |
| 111 | GFPT2 | 179740867 | 0.7258763 | 0.6576121 | 0.2623807 | 0.6275811 |
| 113 | GFPT2 | 179740855 | 0.7636966 | 0.7038407 | 0.2623807 | 0.6275811 |
| 49 | RNF39 | 30039415 | 0.2872570 | 0.3286858 | 0.2725096 | 0.6275811 |
| 25 | RNF39 | 30039232 | 0.2412211 | 0.2765787 | 0.2756029 | 0.6275811 |
| 43 | RNF39 | 30039313 | 0.2391492 | 0.2898949 | 0.2836834 | 0.6275811 |
| 95 | GFPT2 | 179741008 | 0.5458332 | 0.4843944 | 0.2857937 | 0.6275811 |
| 98 | GFPT2 | 179740992 | 0.6218308 | 0.5598780 | 0.2857937 | 0.6275811 |
| 117 | GFPT2 | 179740825 | 0.7615307 | 0.6970619 | 0.2857937 | 0.6275811 |
| 79 | EIF2AK2 | 37383713 | 0.0118696 | 0.0076138 | 0.2890215 | 0.6275811 |
| 7 | MX1 | 42798781 | 0.1233523 | 0.1345820 | 0.2938959 | 0.6275811 |
| 150 | UPK3B | 76145689 | 0.4091882 | 0.3921679 | 0.2969910 | 0.6275811 |
| 96 | GFPT2 | 179740999 | 0.6203808 | 0.5572977 | 0.3021474 | 0.6275811 |
| 115 | GFPT2 | 179740840 | 0.7503077 | 0.6829977 | 0.3021474 | 0.6275811 |
| 24 | RNF39 | 30039208 | 0.1906980 | 0.2166896 | 0.3054799 | 0.6275811 |
| 39 | RNF39 | 30039274 | 0.2189513 | 0.2734733 | 0.3088587 | 0.6275811 |
| 42 | RNF39 | 30039307 | 0.1771945 | 0.2349002 | 0.3175620 | 0.6275811 |
| 4 | MX1 | 42798733 | 0.0449783 | 0.0506473 | 0.3199628 | 0.6275811 |
| 118 | GFPT2 | 179740822 | 0.7255467 | 0.6609020 | 0.3199628 | 0.6275811 |
| 142 | HLA-DPB1 | 33048602 | 0.4550854 | 0.5938896 | 0.3199802 | 0.6275811 |
| 57 | HOOK2 | 12877235 | 0.3353043 | 0.3714093 | 0.3250936 | 0.6275811 |
| 38 | RNF39 | 30039271 | 0.2125212 | 0.2627923 | 0.3264212 | 0.6275811 |
| 58 | HOOK2 | 12877276 | 0.2293970 | 0.2671606 | 0.3335584 | 0.6275811 |
| 76 | EIF2AK2 | 37383588 | 0.1093809 | 0.1141754 | 0.3341666 | 0.6275811 |
| 80 | EIF2AK2 | 37383730 | 0.0288894 | 0.0340524 | 0.3398926 | 0.6296494 |
| 73 | GFPT2 | 179741060 | 0.6451812 | 0.5746584 | 0.3446061 | 0.6296494 |
| 139 | HLA-DPB1 | 33048575 | 0.9091051 | 0.9567140 | 0.3475338 | 0.6296494 |
| 143 | IFI44L | 79085647 | 0.1747650 | 0.2059993 | 0.3578290 | 0.6407635 |
| 23 | RNF39 | 30039206 | 0.1813594 | 0.2108971 | 0.3634106 | 0.6432786 |
| 138 | HLA-DPB1 | 33048571 | 0.9044165 | 0.9467651 | 0.3753325 | 0.6568318 |
| 10 | MX1 | 42798818 | 0.1505739 | 0.1598394 | 0.3831169 | 0.6629214 |
| 121 | FAM132A | 1178192 | 0.8928645 | 0.8958672 | 0.3927697 | 0.6720725 |
| 3 | MX1 | 42798723 | 0.0658323 | 0.0700709 | 0.4027320 | 0.6815465 |
| 68 | HELZ2 | 62199061 | 0.0389775 | 0.0335129 | 0.4176932 | 0.6991821 |
| 54 | HOOK2 | 12877138 | 0.2519799 | 0.2828210 | 0.4356765 | 0.7214427 |
| 17 | RNF39 | 30039127 | 0.3894824 | 0.3731225 | 0.4516335 | 0.7399103 |
| 22 | RNF39 | 30039202 | 0.2191423 | 0.2456934 | 0.4665199 | 0.7562533 |
| 26 | RNF39 | 30039235 | 0.2208101 | 0.2488515 | 0.5002878 | 0.7891718 |
| 123 | FAM132A | 1178172 | 0.8193061 | 0.8278377 | 0.5002878 | 0.7891718 |
| 129 | FAM132A | 1178086 | 0.9048460 | 0.8976444 | 0.5079658 | 0.7891718 |
| 1 | MX1 | 42798695 | 0.0521433 | 0.0489980 | 0.5092635 | 0.7891718 |
| 132 | HLA-DPB1 | 33048423 | 0.9132301 | 0.9505762 | 0.5196934 | 0.7891718 |
| 119 | FAM132A | 1178207 | 0.8051401 | 0.8002057 | 0.5255572 | 0.7891718 |
| 135 | HLA-DPB1 | 33048542 | 0.0688653 | 0.0839724 | 0.5331882 | 0.7891718 |
| 140 | HLA-DPB1 | 33048581 | 0.8955914 | 0.9389990 | 0.5334663 | 0.7891718 |
| 56 | HOOK2 | 12877215 | 0.2742889 | 0.3040664 | 0.5421412 | 0.7891718 |
| 27 | RNF39 | 30039239 | 0.3743278 | 0.3984258 | 0.5434550 | 0.7891718 |
| 20 | RNF39 | 30039158 | 0.1510334 | 0.1669710 | 0.5472100 | 0.7891718 |
| 91 | HOOK2 | 12876937 | 0.2200042 | 0.2565081 | 0.5534452 | 0.7891718 |
| 94 | HOOK2 | 12876911 | 0.2664089 | 0.3049543 | 0.5534452 | 0.7891718 |
| 147 | UPK3B | 76145717 | 0.4805704 | 0.4732804 | 0.5592647 | 0.7901538 |
| 51 | IFITM1 | 313408 | 0.1861145 | 0.1866750 | 0.5837457 | 0.8098814 |
| 126 | FAM132A | 1178136 | 0.9681518 | 0.9694773 | 0.5837457 | 0.8098814 |
| 34 | SMAD3 | 67361798 | 0.9436187 | 0.9274174 | 0.6042510 | 0.8308451 |
| 62 | BRDT | 92414751 | 0.5054684 | 0.4788894 | 0.6213551 | 0.8468025 |
| 55 | HOOK2 | 12877201 | 0.3137922 | 0.3389160 | 0.6477159 | 0.8680289 |
| 19 | RNF39 | 30039132 | 0.1468104 | 0.1601234 | 0.6502388 | 0.8680289 |
| 89 | HOOK2 | 12876944 | 0.2273296 | 0.2659038 | 0.6599430 | 0.8680289 |
| 64 | BRDT | 92414793 | 0.5605071 | 0.5366430 | 0.6699389 | 0.8680289 |
| 127 | FAM132A | 1178118 | 0.9435336 | 0.9412087 | 0.6765643 | 0.8680289 |
| 60 | BRDT | 92414661 | 0.4353187 | 0.4071912 | 0.6832095 | 0.8680289 |
| 87 | HOOK2 | 12876948 | 0.2284571 | 0.2624347 | 0.6846633 | 0.8680289 |
| 120 | FAM132A | 1178202 | 0.7223557 | 0.7274506 | 0.6862044 | 0.8680289 |
| 78 | EIF2AK2 | 37383679 | 0.0151014 | 0.0161317 | 0.6876593 | 0.8680289 |
| 36 | SMAD3 | 67361896 | 0.9011689 | 0.8938339 | 0.7036189 | 0.8809537 |
| 5 | MX1 | 42798749 | 0.0419203 | 0.0423275 | 0.7185415 | 0.8923822 |
| 153 | UPK3B | 76145606 | 0.4234001 | 0.4140856 | 0.7303898 | 0.8970734 |
| 152 | UPK3B | 76145620 | 0.8073974 | 0.8091339 | 0.7372189 | 0.8970734 |
| 148 | UPK3B | 76145702 | 0.3263160 | 0.3185503 | 0.7397943 | 0.8970734 |
| 61 | BRDT | 92414719 | 0.3011353 | 0.2957146 | 0.7647386 | 0.9145581 |
| 144 | IFITM1 | 312419 | 0.0919347 | 0.1019998 | 0.7721429 | 0.9145581 |
| 124 | FAM132A | 1178162 | 0.7826432 | 0.7817024 | 0.7808315 | 0.9145581 |
| 35 | SMAD3 | 67361821 | 0.9322478 | 0.9361443 | 0.7834223 | 0.9145581 |
| 47 | RNF39 | 30039364 | 0.1371199 | 0.1401614 | 0.7946507 | 0.9145581 |
| 146 | IFITM1 | 312463 | 0.1617244 | 0.1586609 | 0.7967807 | 0.9145581 |
| 6 | MX1 | 42798765 | 0.0488478 | 0.0470983 | 0.7988268 | 0.9145581 |
| 18 | RNF39 | 30039130 | 0.2177503 | 0.2308035 | 0.8065675 | 0.9145581 |
| 82 | HOOK2 | 12877020 | 0.2134993 | 0.2465793 | 0.8128033 | 0.9145581 |
| 63 | BRDT | 92414770 | 0.5120284 | 0.4928876 | 0.8136004 | 0.9145581 |
| 85 | HOOK2 | 12876987 | 0.2178240 | 0.2545267 | 0.8259565 | 0.9217195 |
| 88 | HOOK2 | 12876946 | 0.2236624 | 0.2610126 | 0.8391577 | 0.9297143 |
| 59 | BRDT | 92414650 | 0.3600865 | 0.3381310 | 0.8560755 | 0.9416830 |
| 122 | FAM132A | 1178182 | 0.7392234 | 0.7345481 | 0.8646147 | 0.9443310 |
| 92 | HOOK2 | 12876926 | 0.2311439 | 0.2694612 | 0.8923717 | 0.9652470 |
| 81 | TLR1 | 38805839 | 0.0862660 | 0.0654668 | 0.9004698 | 0.9652470 |
| 86 | HOOK2 | 12876969 | 0.2223231 | 0.2589791 | 0.9057593 | 0.9652470 |
| 130 | BRDT | 92418017 | 0.9714090 | 0.9726775 | 0.9151402 | 0.9652470 |
| 84 | HOOK2 | 12876993 | 0.2123469 | 0.2469626 | 0.9191733 | 0.9652470 |
| 21 | RNF39 | 30039186 | 0.2219051 | 0.2303945 | 0.9213721 | 0.9652470 |
| 83 | HOOK2 | 12876997 | 0.2033761 | 0.2362756 | 0.9326098 | 0.9670314 |
| 16 | RNF39 | 30039123 | 0.4496789 | 0.4575020 | 0.9356343 | 0.9670314 |
| 77 | EIF2AK2 | 37383623 | 0.0174223 | 0.0172126 | 0.9627358 | 0.9841293 |
| 2 | MX1 | 42798698 | 0.0454972 | 0.0458381 | 0.9649580 | 0.9841293 |
| 90 | HOOK2 | 12876942 | 0.2311652 | 0.2689455 | 0.9865068 | 0.9936200 |
| 145 | IFITM1 | 312434 | 0.2011502 | 0.1993537 | 0.9871679 | 0.9936200 |
| 93 | HOOK2 | 12876918 | 0.2415910 | 0.2814326 | 1.0000000 | 1.0000000 |
3.4.2.2 Figure17: The Differential methylated CpGsites between dcSSc patients and Controls
[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 17 in our analysis."
3.4.3 Validation of differential methylated CpGsites between lcSSc patients and Controls
3.4.3.1 Table 20: The Differential methylated CpGsites between lcSSc patients and Controls
| Gene | Pos | Mean.CD8.lc | Mean.CD8.NC | P.value.CD8.lc.NC | FDR | |
|---|---|---|---|---|---|---|
| 9 | MX1 | 42798816 | 0.1451567 | 0.2208034 | 0.0000090 | 0.0008554 |
| 12 | MX1 | 42798837 | 0.0921364 | 0.1505124 | 0.0000111 | 0.0008554 |
| 14 | MX1 | 42798857 | 0.1630061 | 0.2552752 | 0.0000323 | 0.0010596 |
| 15 | MX1 | 42798863 | 0.1906832 | 0.2972670 | 0.0000323 | 0.0010596 |
| 11 | MX1 | 42798829 | 0.1424000 | 0.2197405 | 0.0000344 | 0.0010596 |
| 10 | MX1 | 42798818 | 0.1020396 | 0.1598394 | 0.0000444 | 0.0011384 |
| 8 | MX1 | 42798813 | 0.1552502 | 0.2377021 | 0.0000918 | 0.0020185 |
| 7 | MX1 | 42798781 | 0.0931382 | 0.1345820 | 0.0001174 | 0.0022595 |
| 13 | MX1 | 42798847 | 0.1681307 | 0.2580407 | 0.0002393 | 0.0038048 |
| 78 | EIF2AK2 | 37383679 | 0.0105629 | 0.0161317 | 0.0002471 | 0.0038048 |
| 4 | MX1 | 42798733 | 0.0374825 | 0.0506473 | 0.0003426 | 0.0047968 |
| 6 | MX1 | 42798765 | 0.0358928 | 0.0470983 | 0.0003930 | 0.0050436 |
| 5 | MX1 | 42798749 | 0.0319166 | 0.0423275 | 0.0009652 | 0.0114337 |
| 80 | EIF2AK2 | 37383730 | 0.0224456 | 0.0340524 | 0.0032162 | 0.0353777 |
| 76 | EIF2AK2 | 37383588 | 0.0858059 | 0.1141754 | 0.0107400 | 0.1102637 |
| 143 | IFI44L | 79085647 | 0.1654684 | 0.2059993 | 0.0120053 | 0.1123128 |
| 3 | MX1 | 42798723 | 0.0588032 | 0.0700709 | 0.0130194 | 0.1123128 |
| 50 | RNF39 | 30039418 | 0.4368291 | 0.5283172 | 0.0131275 | 0.1123128 |
| 144 | IFITM1 | 312419 | 0.0633512 | 0.1019998 | 0.0166821 | 0.1352131 |
| 77 | EIF2AK2 | 37383623 | 0.0136245 | 0.0172126 | 0.0199767 | 0.1538209 |
| 1 | MX1 | 42798695 | 0.0433350 | 0.0489980 | 0.0255921 | 0.1876758 |
| 48 | RNF39 | 30039411 | 0.4386664 | 0.5018491 | 0.0570498 | 0.3992447 |
| 146 | IFITM1 | 312463 | 0.1273669 | 0.1586609 | 0.0626705 | 0.3992447 |
| 2 | MX1 | 42798698 | 0.0391284 | 0.0458381 | 0.0664892 | 0.3992447 |
| 47 | RNF39 | 30039364 | 0.1604995 | 0.1401614 | 0.0669090 | 0.3992447 |
| 131 | HLA-DPB1 | 33048417 | 0.9160670 | 0.9399218 | 0.0674049 | 0.3992447 |
| 139 | HLA-DPB1 | 33048575 | 0.9340088 | 0.9567140 | 0.0727966 | 0.4139094 |
| 45 | RNF39 | 30039349 | 0.2376113 | 0.3019271 | 0.0752563 | 0.4139094 |
| 44 | RNF39 | 30039323 | 0.2873683 | 0.3438164 | 0.0820504 | 0.4357160 |
| 51 | IFITM1 | 313408 | 0.1705007 | 0.1866750 | 0.0893258 | 0.4585393 |
| 42 | RNF39 | 30039307 | 0.1703290 | 0.2349002 | 0.0955803 | 0.4748180 |
| 145 | IFITM1 | 312434 | 0.1643440 | 0.1993537 | 0.1029896 | 0.4956375 |
| 46 | RNF39 | 30039354 | 0.2416944 | 0.3102584 | 0.1142521 | 0.5331762 |
| 141 | HLA-DPB1 | 33048592 | 0.9408180 | 0.9615786 | 0.1210582 | 0.5483223 |
| 125 | FAM132A | 1178150 | 0.9027851 | 0.9091035 | 0.1442609 | 0.6347479 |
| 138 | HLA-DPB1 | 33048571 | 0.9229893 | 0.9467651 | 0.1564542 | 0.6484039 |
| 49 | RNF39 | 30039415 | 0.2830408 | 0.3286858 | 0.1622257 | 0.6484039 |
| 40 | RNF39 | 30039278 | 0.3906782 | 0.4356661 | 0.1633218 | 0.6484039 |
| 43 | RNF39 | 30039313 | 0.2359025 | 0.2898949 | 0.1642062 | 0.6484039 |
| 79 | EIF2AK2 | 37383713 | 0.0062297 | 0.0076138 | 0.2353836 | 0.9062268 |
| 52 | HOOK2 | 12877099 | 0.2355685 | 0.2514190 | 0.2514498 | 0.9216707 |
| 41 | RNF39 | 30039303 | 0.2192596 | 0.2680066 | 0.2590672 | 0.9216707 |
| 140 | HLA-DPB1 | 33048581 | 0.9175717 | 0.9389990 | 0.2610302 | 0.9216707 |
| 149 | UPK3B | 76145693 | 0.5680260 | 0.5530011 | 0.2674674 | 0.9216707 |
| 39 | RNF39 | 30039274 | 0.2283204 | 0.2734733 | 0.2731704 | 0.9216707 |
| 66 | COX7A2 | 75954118 | 0.5089567 | 0.4770666 | 0.2753042 | 0.9216707 |
| 65 | COX7A2 | 75954022 | 0.5693682 | 0.5349920 | 0.3177918 | 0.9911496 |
| 134 | HLA-DPB1 | 33048444 | 0.8921524 | 0.9096903 | 0.3215650 | 0.9911496 |
| 150 | UPK3B | 76145689 | 0.4044889 | 0.3921679 | 0.3314886 | 0.9911496 |
| 152 | UPK3B | 76145620 | 0.8224503 | 0.8091339 | 0.3372318 | 0.9911496 |
| 29 | COX7A2 | 75953829 | 0.2109157 | 0.1911202 | 0.3512707 | 0.9911496 |
| 68 | HELZ2 | 62199061 | 0.0418837 | 0.0335129 | 0.3524144 | 0.9911496 |
| 53 | HOOK2 | 12877107 | 0.2393899 | 0.2541165 | 0.3877290 | 0.9911496 |
| 154 | UPK3B | 76145589 | 0.2028450 | 0.1890741 | 0.4158312 | 0.9911496 |
| 67 | COX7A2 | 75954122 | 0.4752669 | 0.4490352 | 0.4375967 | 0.9911496 |
| 35 | SMAD3 | 67361821 | 0.9362776 | 0.9361443 | 0.4445705 | 0.9911496 |
| 34 | SMAD3 | 67361798 | 0.9337478 | 0.9274174 | 0.4697180 | 0.9911496 |
| 38 | RNF39 | 30039271 | 0.2314384 | 0.2627923 | 0.4935262 | 0.9911496 |
| 94 | HOOK2 | 12876911 | 0.2886766 | 0.3049543 | 0.4938880 | 0.9911496 |
| 137 | HLA-DPB1 | 33048549 | 0.9227604 | 0.9341162 | 0.4983199 | 0.9911496 |
| 136 | HLA-DPB1 | 33048544 | 0.9425184 | 0.9584988 | 0.5025949 | 0.9911496 |
| 54 | HOOK2 | 12877138 | 0.2716501 | 0.2828210 | 0.5102116 | 0.9911496 |
| 130 | BRDT | 92418017 | 0.9746152 | 0.9726775 | 0.5102116 | 0.9911496 |
| 36 | SMAD3 | 67361896 | 0.8989773 | 0.8938339 | 0.5149527 | 0.9911496 |
| 30 | COX7A2 | 75953883 | 0.2160649 | 0.2034265 | 0.5158519 | 0.9911496 |
| 64 | BRDT | 92414793 | 0.5714565 | 0.5366430 | 0.5287412 | 0.9911496 |
| 31 | COX7A2 | 75953937 | 0.1415766 | 0.1354768 | 0.5333464 | 0.9911496 |
| 32 | COX7A2 | 75953960 | 0.2541696 | 0.2463432 | 0.5333464 | 0.9911496 |
| 62 | BRDT | 92414751 | 0.5087828 | 0.4788894 | 0.5356710 | 0.9911496 |
| 28 | COX7A2 | 75953821 | 0.0875956 | 0.0821239 | 0.5511314 | 0.9911496 |
| 123 | FAM132A | 1178172 | 0.8277238 | 0.8278377 | 0.5884961 | 0.9911496 |
| 121 | FAM132A | 1178192 | 0.9022461 | 0.8958672 | 0.6157679 | 0.9911496 |
| 128 | FAM132A | 1178105 | 0.9778209 | 0.9761999 | 0.6157679 | 0.9911496 |
| 126 | FAM132A | 1178136 | 0.9679960 | 0.9694773 | 0.6249785 | 0.9911496 |
| 63 | BRDT | 92414770 | 0.5148409 | 0.4928876 | 0.6342472 | 0.9911496 |
| 19 | RNF39 | 30039132 | 0.1563233 | 0.1601234 | 0.6366151 | 0.9911496 |
| 33 | COX7A2 | 75953974 | 0.2699570 | 0.2586032 | 0.6537553 | 0.9911496 |
| 17 | RNF39 | 30039127 | 0.3808942 | 0.3731225 | 0.6602062 | 0.9911496 |
| 58 | HOOK2 | 12877276 | 0.2577653 | 0.2671606 | 0.6685840 | 0.9911496 |
| 127 | FAM132A | 1178118 | 0.9400499 | 0.9412087 | 0.6718784 | 0.9911496 |
| 55 | HOOK2 | 12877201 | 0.3270499 | 0.3389160 | 0.6873059 | 0.9911496 |
| 105 | GFPT2 | 179740920 | 0.5592024 | 0.5588129 | 0.6873059 | 0.9911496 |
| 84 | HOOK2 | 12876993 | 0.2326949 | 0.2469626 | 0.6967390 | 0.9911496 |
| 25 | RNF39 | 30039232 | 0.2671077 | 0.2765787 | 0.7006501 | 0.9911496 |
| 148 | UPK3B | 76145702 | 0.3162807 | 0.3185503 | 0.7035164 | 0.9911496 |
| 142 | HLA-DPB1 | 33048602 | 0.5601226 | 0.5938896 | 0.7062118 | 0.9911496 |
| 83 | HOOK2 | 12876997 | 0.2247642 | 0.2362756 | 0.7062186 | 0.9911496 |
| 82 | HOOK2 | 12877020 | 0.2345430 | 0.2465793 | 0.7253119 | 0.9911496 |
| 93 | HOOK2 | 12876918 | 0.2674003 | 0.2814326 | 0.7349230 | 0.9911496 |
| 18 | RNF39 | 30039130 | 0.2204855 | 0.2308035 | 0.7378947 | 0.9911496 |
| 16 | RNF39 | 30039123 | 0.4621913 | 0.4575020 | 0.7594439 | 0.9911496 |
| 74 | GFPT2 | 179741042 | 0.4196268 | 0.4307610 | 0.7594439 | 0.9911496 |
| 61 | BRDT | 92414719 | 0.2798224 | 0.2957146 | 0.7677854 | 0.9911496 |
| 100 | GFPT2 | 179740963 | 0.5783309 | 0.5755657 | 0.7737639 | 0.9911496 |
| 117 | GFPT2 | 179740825 | 0.6912174 | 0.6970619 | 0.7737639 | 0.9911496 |
| 75 | GFPT2 | 179741039 | 0.5602058 | 0.5738683 | 0.7793699 | 0.9911496 |
| 37 | HLA-DPB1 | 33048370 | 0.7607485 | 0.7459280 | 0.7835663 | 0.9911496 |
| 103 | GFPT2 | 179740940 | 0.5575250 | 0.5537678 | 0.7835663 | 0.9911496 |
| 85 | HOOK2 | 12876987 | 0.2403014 | 0.2545267 | 0.8032715 | 0.9911496 |
| 120 | FAM132A | 1178202 | 0.7360413 | 0.7274506 | 0.8081759 | 0.9911496 |
| 69 | GFPT2 | 179741101 | 0.5525242 | 0.5436586 | 0.8095248 | 0.9911496 |
| 89 | HOOK2 | 12876944 | 0.2503907 | 0.2659038 | 0.8131714 | 0.9911496 |
| 92 | HOOK2 | 12876926 | 0.2543572 | 0.2694612 | 0.8131714 | 0.9911496 |
| 20 | RNF39 | 30039158 | 0.1684117 | 0.1669710 | 0.8132633 | 0.9911496 |
| 90 | HOOK2 | 12876942 | 0.2537722 | 0.2689455 | 0.8231007 | 0.9911496 |
| 116 | GFPT2 | 179740832 | 0.6948595 | 0.6991309 | 0.8231007 | 0.9911496 |
| 133 | HLA-DPB1 | 33048433 | 0.9352510 | 0.9465281 | 0.8286707 | 0.9911496 |
| 119 | FAM132A | 1178207 | 0.7984435 | 0.8002057 | 0.8297871 | 0.9911496 |
| 122 | FAM132A | 1178182 | 0.7395861 | 0.7345481 | 0.8297871 | 0.9911496 |
| 56 | HOOK2 | 12877215 | 0.2915891 | 0.3040664 | 0.8330581 | 0.9911496 |
| 57 | HOOK2 | 12877235 | 0.3606170 | 0.3714093 | 0.8330581 | 0.9911496 |
| 86 | HOOK2 | 12876969 | 0.2438928 | 0.2589791 | 0.8330581 | 0.9911496 |
| 98 | GFPT2 | 179740992 | 0.5593665 | 0.5598780 | 0.8330581 | 0.9911496 |
| 27 | RNF39 | 30039239 | 0.4031679 | 0.3984258 | 0.8388078 | 0.9911496 |
| 60 | BRDT | 92414661 | 0.4161603 | 0.4071912 | 0.8490843 | 0.9911496 |
| 97 | GFPT2 | 179740994 | 0.5698766 | 0.5692321 | 0.8530507 | 0.9911496 |
| 108 | GFPT2 | 179740900 | 0.5604640 | 0.5621152 | 0.8530507 | 0.9911496 |
| 113 | GFPT2 | 179740855 | 0.6979854 | 0.7038407 | 0.8530507 | 0.9911496 |
| 147 | UPK3B | 76145717 | 0.4812723 | 0.4732804 | 0.8542274 | 0.9911496 |
| 107 | GFPT2 | 179740906 | 0.5964612 | 0.5964526 | 0.8630829 | 0.9911496 |
| 101 | GFPT2 | 179740957 | 0.5923485 | 0.5937250 | 0.8731368 | 0.9911496 |
| 59 | BRDT | 92414650 | 0.3375857 | 0.3381310 | 0.8809049 | 0.9911496 |
| 99 | GFPT2 | 179740970 | 0.5221365 | 0.5222309 | 0.8832110 | 0.9911496 |
| 112 | GFPT2 | 179740861 | 0.6805505 | 0.6855562 | 0.8832110 | 0.9911496 |
| 151 | UPK3B | 76145628 | 0.7452686 | 0.7505882 | 0.8955871 | 0.9911496 |
| 71 | GFPT2 | 179741067 | 0.5131640 | 0.5217057 | 0.9015021 | 0.9911496 |
| 88 | HOOK2 | 12876946 | 0.2482356 | 0.2610126 | 0.9034137 | 0.9911496 |
| 96 | GFPT2 | 179740999 | 0.5553063 | 0.5572977 | 0.9034137 | 0.9911496 |
| 21 | RNF39 | 30039186 | 0.2363932 | 0.2303945 | 0.9059812 | 0.9911496 |
| 132 | HLA-DPB1 | 33048423 | 0.9402103 | 0.9505762 | 0.9110651 | 0.9911496 |
| 70 | GFPT2 | 179741081 | 0.5358414 | 0.5435904 | 0.9118262 | 0.9911496 |
| 106 | GFPT2 | 179740918 | 0.5761280 | 0.5829248 | 0.9135391 | 0.9911496 |
| 111 | GFPT2 | 179740867 | 0.6549886 | 0.6576121 | 0.9135391 | 0.9911496 |
| 95 | GFPT2 | 179741008 | 0.4810771 | 0.4843944 | 0.9236783 | 0.9911496 |
| 118 | GFPT2 | 179740822 | 0.6573863 | 0.6609020 | 0.9236783 | 0.9911496 |
| 81 | TLR1 | 38805839 | 0.0720627 | 0.0654668 | 0.9301954 | 0.9911496 |
| 135 | HLA-DPB1 | 33048542 | 0.0603714 | 0.0839724 | 0.9387683 | 0.9911496 |
| 72 | GFPT2 | 179741063 | 0.5055341 | 0.5105164 | 0.9428796 | 0.9911496 |
| 124 | FAM132A | 1178162 | 0.7907324 | 0.7817024 | 0.9428796 | 0.9911496 |
| 115 | GFPT2 | 179740840 | 0.6761512 | 0.6829977 | 0.9439917 | 0.9911496 |
| 24 | RNF39 | 30039208 | 0.2224265 | 0.2166896 | 0.9529086 | 0.9911496 |
| 22 | RNF39 | 30039202 | 0.2489331 | 0.2456934 | 0.9532521 | 0.9911496 |
| 73 | GFPT2 | 179741060 | 0.5687054 | 0.5746584 | 0.9532521 | 0.9911496 |
| 102 | GFPT2 | 179740955 | 0.5964764 | 0.5986114 | 0.9541628 | 0.9911496 |
| 87 | HOOK2 | 12876948 | 0.2494365 | 0.2624347 | 0.9643412 | 0.9911496 |
| 104 | GFPT2 | 179740935 | 0.5994408 | 0.5997596 | 0.9643412 | 0.9911496 |
| 110 | GFPT2 | 179740869 | 0.6609613 | 0.6635659 | 0.9643412 | 0.9911496 |
| 129 | FAM132A | 1178086 | 0.9001452 | 0.8976444 | 0.9738276 | 0.9911496 |
| 26 | RNF39 | 30039235 | 0.2505794 | 0.2488515 | 0.9740188 | 0.9911496 |
| 153 | UPK3B | 76145606 | 0.4142247 | 0.4140856 | 0.9740188 | 0.9911496 |
| 114 | GFPT2 | 179740852 | 0.6588486 | 0.6570538 | 0.9745253 | 0.9911496 |
| 23 | RNF39 | 30039206 | 0.2145289 | 0.2108971 | 0.9790607 | 0.9911496 |
| 91 | HOOK2 | 12876937 | 0.2434971 | 0.2565081 | 0.9847136 | 0.9911496 |
| 109 | GFPT2 | 179740888 | 0.5610022 | 0.5645584 | 0.9949042 | 0.9949042 |
3.4.3.2 Figure18: The Differential methylated CpGsites between lcSSc patients and Controls
[1] "The number of significant differential methylated CpGsites between lcSSc patients and normal controls in CD8+ T cells is 14"
[1] "Plot the figure of MX1 42798816"
[1] "Plot the figure of MX1 42798837"
[1] "Plot the figure of MX1 42798857"
[1] "Plot the figure of MX1 42798863"
[1] "Plot the figure of MX1 42798829"
[1] "Plot the figure of MX1 42798818"
[1] "Plot the figure of MX1 42798813"
[1] "Plot the figure of MX1 42798781"
[1] "Plot the figure of MX1 42798847"
[1] "Plot the figure of EIF2AK2 37383679"
[1] "Plot the figure of MX1 42798733"
[1] "Plot the figure of MX1 42798765"
[1] "Plot the figure of MX1 42798749"
[1] "Plot the figure of EIF2AK2 37383730"
3.4.4 Validation of differential methylated CpGsites between dcSSc patients and lcSSc patients
3.4.4.1 Table 21: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
| Gene | Pos | Mean.CD8.dc | Mean.CD8.lc | P.value.CD8.dc.lc | FDR | |
|---|---|---|---|---|---|---|
| 6 | MX1 | 42798765 | 0.0488478 | 0.0358928 | 0.0099600 | 0.2785737 |
| 66 | COX7A2 | 75954118 | 0.4232681 | 0.5089567 | 0.0112671 | 0.2785737 |
| 11 | MX1 | 42798829 | 0.2007530 | 0.1424000 | 0.0121899 | 0.2785737 |
| 10 | MX1 | 42798818 | 0.1505739 | 0.1020396 | 0.0131771 | 0.2785737 |
| 65 | COX7A2 | 75954022 | 0.4671704 | 0.5693682 | 0.0131771 | 0.2785737 |
| 30 | COX7A2 | 75953883 | 0.1609718 | 0.2160649 | 0.0149799 | 0.2785737 |
| 67 | COX7A2 | 75954122 | 0.3900427 | 0.4752669 | 0.0184208 | 0.2785737 |
| 9 | MX1 | 42798816 | 0.2059071 | 0.1451567 | 0.0222112 | 0.2785737 |
| 12 | MX1 | 42798837 | 0.1306970 | 0.0921364 | 0.0222112 | 0.2785737 |
| 31 | COX7A2 | 75953937 | 0.1020046 | 0.1415766 | 0.0241357 | 0.2785737 |
| 8 | MX1 | 42798813 | 0.2192756 | 0.1552502 | 0.0255997 | 0.2785737 |
| 15 | MX1 | 42798863 | 0.2567028 | 0.1906832 | 0.0255997 | 0.2785737 |
| 79 | EIF2AK2 | 37383713 | 0.0118696 | 0.0062297 | 0.0260472 | 0.2785737 |
| 7 | MX1 | 42798781 | 0.1233523 | 0.0931382 | 0.0274510 | 0.2785737 |
| 14 | MX1 | 42798857 | 0.2210567 | 0.1630061 | 0.0274510 | 0.2785737 |
| 5 | MX1 | 42798749 | 0.0419203 | 0.0319166 | 0.0314925 | 0.2785737 |
| 29 | COX7A2 | 75953829 | 0.1553651 | 0.2109157 | 0.0325606 | 0.2785737 |
| 33 | COX7A2 | 75953974 | 0.2048235 | 0.2699570 | 0.0325606 | 0.2785737 |
| 37 | HLA-DPB1 | 33048370 | 0.6872302 | 0.7607485 | 0.0360196 | 0.2896434 |
| 32 | COX7A2 | 75953960 | 0.1962902 | 0.2541696 | 0.0376160 | 0.2896434 |
| 78 | EIF2AK2 | 37383679 | 0.0151014 | 0.0105629 | 0.0433046 | 0.3175667 |
| 28 | COX7A2 | 75953821 | 0.0618621 | 0.0875956 | 0.0464036 | 0.3248253 |
| 1 | MX1 | 42798695 | 0.0521433 | 0.0433350 | 0.0505153 | 0.3382332 |
| 151 | UPK3B | 76145628 | 0.7168508 | 0.7452686 | 0.0536474 | 0.3442377 |
| 13 | MX1 | 42798847 | 0.2248944 | 0.1681307 | 0.0758536 | 0.4636141 |
| 77 | EIF2AK2 | 37383623 | 0.0174223 | 0.0136245 | 0.0782725 | 0.4636141 |
| 144 | IFITM1 | 312419 | 0.0919347 | 0.0633512 | 0.0826675 | 0.4715109 |
| 80 | EIF2AK2 | 37383730 | 0.0288894 | 0.0224456 | 0.0884798 | 0.4866390 |
| 2 | MX1 | 42798698 | 0.0454972 | 0.0391284 | 0.1060290 | 0.5630507 |
| 47 | RNF39 | 30039364 | 0.1371199 | 0.1604995 | 0.1118556 | 0.5741920 |
| 4 | MX1 | 42798733 | 0.0449783 | 0.0374825 | 0.1179255 | 0.5858232 |
| 74 | GFPT2 | 179741042 | 0.5025036 | 0.4196268 | 0.1308176 | 0.6295596 |
| 133 | HLA-DPB1 | 33048433 | 0.9009518 | 0.9352510 | 0.1604089 | 0.6881031 |
| 75 | GFPT2 | 179741039 | 0.6485978 | 0.5602058 | 0.1676838 | 0.6881031 |
| 121 | FAM132A | 1178192 | 0.8928645 | 0.9022461 | 0.1758912 | 0.6881031 |
| 137 | HLA-DPB1 | 33048549 | 0.8846894 | 0.9227604 | 0.1779858 | 0.6881031 |
| 3 | MX1 | 42798723 | 0.0658323 | 0.0588032 | 0.1931756 | 0.6881031 |
| 70 | GFPT2 | 179741081 | 0.6102137 | 0.5358414 | 0.1931756 | 0.6881031 |
| 76 | EIF2AK2 | 37383588 | 0.1093809 | 0.0858059 | 0.2013287 | 0.6881031 |
| 113 | GFPT2 | 179740855 | 0.7636966 | 0.6979854 | 0.2022604 | 0.6881031 |
| 51 | IFITM1 | 313408 | 0.1861145 | 0.1705007 | 0.2116451 | 0.6881031 |
| 112 | GFPT2 | 179740861 | 0.7475890 | 0.6805505 | 0.2116451 | 0.6881031 |
| 114 | GFPT2 | 179740852 | 0.7266582 | 0.6588486 | 0.2116451 | 0.6881031 |
| 109 | GFPT2 | 179740888 | 0.6393397 | 0.5610022 | 0.2213328 | 0.6881031 |
| 71 | GFPT2 | 179741067 | 0.5889373 | 0.5131640 | 0.2313265 | 0.6881031 |
| 115 | GFPT2 | 179740840 | 0.7503077 | 0.6761512 | 0.2313265 | 0.6881031 |
| 116 | GFPT2 | 179740832 | 0.7624362 | 0.6948595 | 0.2416289 | 0.6881031 |
| 117 | GFPT2 | 179740825 | 0.7615307 | 0.6912174 | 0.2416289 | 0.6881031 |
| 146 | IFITM1 | 312463 | 0.1617244 | 0.1273669 | 0.2436558 | 0.6881031 |
| 111 | GFPT2 | 179740867 | 0.7258763 | 0.6549886 | 0.2522421 | 0.6881031 |
| 118 | GFPT2 | 179740822 | 0.7255467 | 0.6573863 | 0.2522421 | 0.6881031 |
| 145 | IFITM1 | 312434 | 0.2011502 | 0.1643440 | 0.2597877 | 0.6881031 |
| 107 | GFPT2 | 179740906 | 0.6717459 | 0.5964612 | 0.2631682 | 0.6881031 |
| 128 | FAM132A | 1178105 | 0.9793370 | 0.9778209 | 0.2631682 | 0.6881031 |
| 72 | GFPT2 | 179741063 | 0.5838811 | 0.5055341 | 0.2744087 | 0.6881031 |
| 104 | GFPT2 | 179740935 | 0.6658861 | 0.5994408 | 0.2744087 | 0.6881031 |
| 108 | GFPT2 | 179740900 | 0.6291681 | 0.5604640 | 0.2744087 | 0.6881031 |
| 110 | GFPT2 | 179740869 | 0.7297972 | 0.6609613 | 0.2744087 | 0.6881031 |
| 136 | HLA-DPB1 | 33048544 | 0.9068650 | 0.9425184 | 0.2748689 | 0.6881031 |
| 152 | UPK3B | 76145620 | 0.8073974 | 0.8224503 | 0.2824113 | 0.6881031 |
| 73 | GFPT2 | 179741060 | 0.6451812 | 0.5687054 | 0.2859649 | 0.6881031 |
| 95 | GFPT2 | 179741008 | 0.5458332 | 0.4810771 | 0.2859649 | 0.6881031 |
| 105 | GFPT2 | 179740920 | 0.6355716 | 0.5592024 | 0.2859649 | 0.6881031 |
| 106 | GFPT2 | 179740918 | 0.6521347 | 0.5761280 | 0.2859649 | 0.6881031 |
| 134 | HLA-DPB1 | 33048444 | 0.8559200 | 0.8921524 | 0.2940729 | 0.6967267 |
| 99 | GFPT2 | 179740970 | 0.5887988 | 0.5221365 | 0.3225341 | 0.7525795 |
| 23 | RNF39 | 30039206 | 0.1813594 | 0.2145289 | 0.3484969 | 0.7741731 |
| 69 | GFPT2 | 179741101 | 0.6244667 | 0.5525242 | 0.3484969 | 0.7741731 |
| 96 | GFPT2 | 179740999 | 0.6203808 | 0.5553063 | 0.3484969 | 0.7741731 |
| 97 | GFPT2 | 179740994 | 0.6334668 | 0.5698766 | 0.3619511 | 0.7741731 |
| 101 | GFPT2 | 179740957 | 0.6589853 | 0.5923485 | 0.3619511 | 0.7741731 |
| 102 | GFPT2 | 179740955 | 0.6632321 | 0.5964764 | 0.3619511 | 0.7741731 |
| 20 | RNF39 | 30039158 | 0.1510334 | 0.1684117 | 0.3757183 | 0.7926113 |
| 25 | RNF39 | 30039232 | 0.2412211 | 0.2671077 | 0.4188760 | 0.8540057 |
| 119 | FAM132A | 1178207 | 0.8051401 | 0.7984435 | 0.4188760 | 0.8540057 |
| 100 | GFPT2 | 179740963 | 0.6408295 | 0.5783309 | 0.4338707 | 0.8540057 |
| 103 | GFPT2 | 179740940 | 0.6219964 | 0.5575250 | 0.4338707 | 0.8540057 |
| 127 | FAM132A | 1178118 | 0.9435336 | 0.9400499 | 0.4338707 | 0.8540057 |
| 89 | HOOK2 | 12876944 | 0.2273296 | 0.2503907 | 0.4380938 | 0.8540057 |
| 56 | HOOK2 | 12877215 | 0.2742889 | 0.2915891 | 0.4528368 | 0.8551919 |
| 24 | RNF39 | 30039208 | 0.1906980 | 0.2224265 | 0.4647508 | 0.8551919 |
| 98 | GFPT2 | 179740992 | 0.6218308 | 0.5593665 | 0.4647508 | 0.8551919 |
| 120 | FAM132A | 1178202 | 0.7223557 | 0.7360413 | 0.4762820 | 0.8551919 |
| 154 | UPK3B | 76145589 | 0.2005878 | 0.2028450 | 0.4762820 | 0.8551919 |
| 22 | RNF39 | 30039202 | 0.2191423 | 0.2489331 | 0.4806271 | 0.8551919 |
| 41 | RNF39 | 30039303 | 0.1952517 | 0.2192596 | 0.4806271 | 0.8551919 |
| 91 | HOOK2 | 12876937 | 0.2200042 | 0.2434971 | 0.4831279 | 0.8551919 |
| 26 | RNF39 | 30039235 | 0.2208101 | 0.2505794 | 0.4967874 | 0.8662903 |
| 27 | RNF39 | 30039239 | 0.3743278 | 0.4031679 | 0.5006483 | 0.8662903 |
| 40 | RNF39 | 30039278 | 0.3615585 | 0.3906782 | 0.5299371 | 0.8977817 |
| 87 | HOOK2 | 12876948 | 0.2284571 | 0.2494365 | 0.5305074 | 0.8977817 |
| 57 | HOOK2 | 12877235 | 0.3353043 | 0.3606170 | 0.5467973 | 0.9123642 |
| 135 | HLA-DPB1 | 33048542 | 0.0688653 | 0.0603714 | 0.5608346 | 0.9123642 |
| 123 | FAM132A | 1178172 | 0.8193061 | 0.8277238 | 0.5641490 | 0.9123642 |
| 38 | RNF39 | 30039271 | 0.2125212 | 0.2314384 | 0.5687888 | 0.9123642 |
| 132 | HLA-DPB1 | 33048423 | 0.9132301 | 0.9402103 | 0.5705938 | 0.9123642 |
| 82 | HOOK2 | 12877020 | 0.2134993 | 0.2345430 | 0.5800855 | 0.9123642 |
| 143 | IFI44L | 79085647 | 0.1747650 | 0.1654684 | 0.5805954 | 0.9123642 |
| 42 | RNF39 | 30039307 | 0.1771945 | 0.1703290 | 0.6135012 | 0.9283074 |
| 85 | HOOK2 | 12876987 | 0.2178240 | 0.2403014 | 0.6142730 | 0.9283074 |
| 52 | HOOK2 | 12877099 | 0.2162453 | 0.2355685 | 0.6316856 | 0.9283074 |
| 58 | HOOK2 | 12877276 | 0.2293970 | 0.2577653 | 0.6316856 | 0.9283074 |
| 84 | HOOK2 | 12876993 | 0.2123469 | 0.2326949 | 0.6316856 | 0.9283074 |
| 17 | RNF39 | 30039127 | 0.3894824 | 0.3808942 | 0.6355221 | 0.9283074 |
| 59 | BRDT | 92414650 | 0.3600865 | 0.3375857 | 0.6355221 | 0.9283074 |
| 141 | HLA-DPB1 | 33048592 | 0.9067151 | 0.9408180 | 0.6500147 | 0.9283074 |
| 61 | BRDT | 92414719 | 0.3011353 | 0.2798224 | 0.6539311 | 0.9283074 |
| 130 | BRDT | 92418017 | 0.9714090 | 0.9746152 | 0.6539311 | 0.9283074 |
| 53 | HOOK2 | 12877107 | 0.2193410 | 0.2393899 | 0.6671087 | 0.9283074 |
| 92 | HOOK2 | 12876926 | 0.2311439 | 0.2543572 | 0.6671087 | 0.9283074 |
| 148 | UPK3B | 76145702 | 0.3263160 | 0.3162807 | 0.6691047 | 0.9283074 |
| 83 | HOOK2 | 12876997 | 0.2033761 | 0.2247642 | 0.6851025 | 0.9420160 |
| 88 | HOOK2 | 12876946 | 0.2236624 | 0.2482356 | 0.7032727 | 0.9445535 |
| 90 | HOOK2 | 12876942 | 0.2311652 | 0.2537722 | 0.7032727 | 0.9445535 |
| 142 | HLA-DPB1 | 33048602 | 0.4550854 | 0.5601226 | 0.7053484 | 0.9445535 |
| 49 | RNF39 | 30039415 | 0.2872570 | 0.2830408 | 0.7295468 | 0.9614919 |
| 16 | RNF39 | 30039123 | 0.4496789 | 0.4621913 | 0.7488942 | 0.9614919 |
| 153 | UPK3B | 76145606 | 0.4234001 | 0.4142247 | 0.7488942 | 0.9614919 |
| 35 | SMAD3 | 67361821 | 0.9322478 | 0.9362776 | 0.7502911 | 0.9614919 |
| 55 | HOOK2 | 12877201 | 0.3137922 | 0.3270499 | 0.7587485 | 0.9614919 |
| 21 | RNF39 | 30039186 | 0.2219051 | 0.2363932 | 0.7683973 | 0.9614919 |
| 122 | FAM132A | 1178182 | 0.7392234 | 0.7395861 | 0.7683973 | 0.9614919 |
| 54 | HOOK2 | 12877138 | 0.2519799 | 0.2716501 | 0.7775298 | 0.9614919 |
| 147 | UPK3B | 76145717 | 0.4805704 | 0.4812723 | 0.7856472 | 0.9614919 |
| 131 | HLA-DPB1 | 33048417 | 0.8982112 | 0.9160670 | 0.7875857 | 0.9614919 |
| 45 | RNF39 | 30039349 | 0.2382702 | 0.2376113 | 0.7880446 | 0.9614919 |
| 126 | FAM132A | 1178136 | 0.9681518 | 0.9679960 | 0.8078245 | 0.9614919 |
| 93 | HOOK2 | 12876918 | 0.2415910 | 0.2674003 | 0.8154662 | 0.9614919 |
| 44 | RNF39 | 30039323 | 0.2900312 | 0.2873683 | 0.8277251 | 0.9614919 |
| 129 | FAM132A | 1178086 | 0.9048460 | 0.9001452 | 0.8277251 | 0.9614919 |
| 81 | TLR1 | 38805839 | 0.0862660 | 0.0720627 | 0.8309871 | 0.9614919 |
| 149 | UPK3B | 76145693 | 0.5693504 | 0.5680260 | 0.8459705 | 0.9614919 |
| 125 | FAM132A | 1178150 | 0.9015033 | 0.9027851 | 0.8477344 | 0.9614919 |
| 48 | RNF39 | 30039411 | 0.4398426 | 0.4386664 | 0.8561231 | 0.9614919 |
| 36 | SMAD3 | 67361896 | 0.9011689 | 0.8989773 | 0.8610559 | 0.9614919 |
| 43 | RNF39 | 30039313 | 0.2391492 | 0.2359025 | 0.8678401 | 0.9614919 |
| 46 | RNF39 | 30039354 | 0.2384689 | 0.2416944 | 0.8678401 | 0.9614919 |
| 64 | BRDT | 92414793 | 0.5605071 | 0.5714565 | 0.8678401 | 0.9614919 |
| 150 | UPK3B | 76145689 | 0.4091882 | 0.4044889 | 0.8678401 | 0.9614919 |
| 94 | HOOK2 | 12876911 | 0.2664089 | 0.2886766 | 0.8925354 | 0.9817889 |
| 60 | BRDT | 92414661 | 0.4353187 | 0.4161603 | 0.9082902 | 0.9821410 |
| 68 | HELZ2 | 62199061 | 0.0389775 | 0.0418837 | 0.9095632 | 0.9821410 |
| 86 | HOOK2 | 12876969 | 0.2223231 | 0.2438928 | 0.9119881 | 0.9821410 |
| 34 | SMAD3 | 67361798 | 0.9436187 | 0.9337478 | 0.9365277 | 0.9874460 |
| 18 | RNF39 | 30039130 | 0.2177503 | 0.2204855 | 0.9483698 | 0.9874460 |
| 50 | RNF39 | 30039418 | 0.4424677 | 0.4368291 | 0.9489740 | 0.9874460 |
| 62 | BRDT | 92414751 | 0.5054684 | 0.5087828 | 0.9489740 | 0.9874460 |
| 124 | FAM132A | 1178162 | 0.7826432 | 0.7907324 | 0.9489740 | 0.9874460 |
| 39 | RNF39 | 30039274 | 0.2189513 | 0.2283204 | 0.9690080 | 0.9952213 |
| 19 | RNF39 | 30039132 | 0.1468104 | 0.1563233 | 0.9693714 | 0.9952213 |
| 139 | HLA-DPB1 | 33048575 | 0.9091051 | 0.9340088 | 0.9773749 | 0.9967929 |
| 140 | HLA-DPB1 | 33048581 | 0.8955914 | 0.9175717 | 0.9886847 | 1.0000000 |
| 63 | BRDT | 92414770 | 0.5120284 | 0.5148409 | 1.0000000 | 1.0000000 |
| 138 | HLA-DPB1 | 33048571 | 0.9044165 | 0.9229893 | 1.0000000 | 1.0000000 |
3.4.4.2 Figure19: The Differential methylated CpGsites between dcSSc patients and lcSSc patients
[1] "As there are no CpGsite showed significant difference between dcSSc patients and lcSSc patients, there is no Figure 19 in our analysis."
3.5 PartII Summary:
Here, In Part II, we conducted the differential methylation analysis with the validation datasets, as we have confirmed its high correlation with the results of DNA methylation 450K. And in our analysis, we divided the CpGsites into two subgroups: The CpGsites shared in the two stages and the CpGsites only in the validaton stage. And we separately calculated and plotted its methylation status in different comparisons as well as in different cell types. We found that the genes such as MX1, EIF2AK2,IFI44L,PARP9 and IFITM1 are the main genes showing differential methylation between cases and controls in CD4+ and CD8+. And all these genes are belong to or associated with the type I interferon pathway, thus confirming and validating our previous GO analysis that the GO term like Type I interferon regulation is associated with SSc. Also, we found that the in the subgroup analysis, especially in dcSSc vs. Control, we can hardly find any significantly differential methylated sites, while in lcSSc vs. Control comparison, we found more significant CpGsites even than in the total SSc vs. Control comparison, indicating the consistency between the lcSSc patients, and also indicating the complexity between the methylation status of the dcSSc patients. Thus, our data suggested that, from the perspective of DNA methylation changes, the lcSSc patients are more consistent than the dcSSc patients, indicating the further exploration of the consistentcy and the uniqueness of the dcSSc epigenetic changes. In addition, we found that there are more significant CpGsites in CD8+ T cells than in the CD4+ T cells’ comparison, indicating the more severely epigenetic changes in CD8+ T cells, which need much more further exploration for its important role in SSc pathogenesis.
4 Part III: Differential gene expression in CD4+/CD8+ T cells and its correlation with gene methylation
4.1 Differential gene expression in CD4+ T cells between SSc patients and Controls
4.1.1 Table 22: The Differential expression between SSc patients and Controls
| Genes | Mean.Case | Mean.Control | Case.CI1 | Case.CI2 | Control.CI1 | Control.CI2 | P.value | FDR |
|---|---|---|---|---|---|---|---|---|
| IFI44L | 8.046350 | 1.273579 | 7.036447 | 9.056254 | 1.231390 | 1.315768 | 0.0198656 | 0.0331093 |
| IFITM1 | 2.870440 | 1.147245 | 2.714960 | 3.025920 | 1.117331 | 1.177160 | 0.0056352 | 0.0140879 |
| MX1 | 2.865622 | 1.185428 | 2.733170 | 2.998075 | 1.155190 | 1.215667 | 0.0296189 | 0.0370236 |
| PARP9 | 6.659666 | 1.430793 | 6.336573 | 6.982759 | 1.381182 | 1.480404 | 0.0004580 | 0.0022900 |
| EIF2AK2 | 1.992502 | 1.120276 | 1.853987 | 2.131017 | 1.064743 | 1.175809 | 0.1230055 | 0.1230055 |
4.1.2 Figure20: The Differential expression between SSc patients and Controls
[1] "Plot the Expression status of IFI44L"
[1] "Plot the Expression status of IFITM1"
[1] "Plot the Expression status of MX1"
[1] "Plot the Expression status of PARP9"
[1] "Plot the Expression status of EIF2AK2"
4.2 Differential gene expression in CD8+ T cells between SSc patients and Controls
4.2.1 Table 23: The Differential expression between SSc patients and Controls
| Genes | Mean.Case | Mean.Control | Case.CI1 | Case.CI2 | Control.CI1 | Control.CI2 | P.value | FDR |
|---|---|---|---|---|---|---|---|---|
| IFI44L | 4.395221 | 1.966491 | 4.055546 | 4.734896 | 1.845879 | 2.087103 | 0.0657267 | 0.0821583 |
| IFITM1 | 1.636151 | 1.076445 | 1.588943 | 1.683359 | 1.059281 | 1.093609 | 0.0202463 | 0.0821583 |
| MX1 | 3.112866 | 1.468340 | 2.952946 | 3.272786 | 1.408011 | 1.528668 | 0.0527902 | 0.0821583 |
| PARP9 | 4.931086 | 1.227470 | 4.530545 | 5.331627 | 1.195379 | 1.259562 | 0.0596821 | 0.0821583 |
| EIF2AK2 | 1.282878 | 1.211615 | 1.215745 | 1.350011 | 1.120513 | 1.302716 | 0.7393644 | 0.7393644 |
4.2.2 Figure21: The Differential expression between SSc patients and Controls
[1] "Plot the Expression status of IFI44L"
[1] "Plot the Expression status of IFITM1"
[1] "Plot the Expression status of MX1"
[1] "Plot the Expression status of PARP9"
[1] "Plot the Expression status of EIF2AK2"
4.3 Correlation between gene expression and methylation in CD4+ T cells
4.3.1 Table 24: The correlation between expression and methylation in CD4+ T cells
| CpGs | Gene | Corr | Corr.p | Lm.r2 |
|---|---|---|---|---|
| 79085586 | IFI44L | -0.39 | 0.0316 | 0.1545703 |
| 79085765 | IFI44L | -0.34 | 0.0640 | 0.1172578 |
| 79085713 | IFI44L | -0.31 | 0.0930 | 0.0975002 |
| 79085647 | IFI44L | -0.24 | 0.1950 | 0.0593440 |
| 312463 | IFITM1 | 0.23 | 0.2350 | 0.0537058 |
| 42798765 | MX1 | -0.20 | 0.2890 | 0.0386963 |
| 42798723 | MX1 | -0.19 | 0.3030 | 0.0364615 |
| 122281975 | PARP9 | -0.19 | 0.3050 | 0.0362413 |
| 42798747 | MX1 | -0.19 | 0.3070 | 0.0360014 |
| 42798698 | MX1 | -0.19 | 0.3190 | 0.0343050 |
| 42798749 | MX1 | -0.18 | 0.3430 | 0.0309958 |
| 42798857 | MX1 | -0.18 | 0.3450 | 0.0307559 |
| 122281939 | PARP9 | -0.15 | 0.4080 | 0.0237587 |
| 42798695 | MX1 | -0.14 | 0.4390 | 0.0207603 |
| 42798863 | MX1 | -0.14 | 0.4530 | 0.0195934 |
| 42798829 | MX1 | -0.13 | 0.4710 | 0.0181008 |
| 42798847 | MX1 | -0.13 | 0.4720 | 0.0179492 |
| 37383623 | EIF2AK2 | 0.28 | 0.4720 | 0.0762774 |
| 42798818 | MX1 | -0.13 | 0.4750 | 0.0177674 |
| 42798816 | MX1 | -0.13 | 0.5010 | 0.0157895 |
| 42798837 | MX1 | -0.12 | 0.5070 | 0.0153241 |
| 37383588 | EIF2AK2 | -0.24 | 0.5340 | 0.0574691 |
| 42798733 | MX1 | -0.10 | 0.5890 | 0.0102004 |
| 42798781 | MX1 | -0.09 | 0.6350 | 0.0078751 |
| 312518 | IFITM1 | 0.14 | 0.6380 | 0.0208792 |
| 313354 | IFITM1 | -0.09 | 0.6440 | 0.0074461 |
| 313408 | IFITM1 | -0.09 | 0.6470 | 0.0073308 |
| 37383713 | EIF2AK2 | 0.14 | 0.7110 | 0.0208512 |
| 37383679 | EIF2AK2 | 0.13 | 0.7400 | 0.0167979 |
| 42798813 | MX1 | -0.05 | 0.7910 | 0.0024505 |
| 37383730 | EIF2AK2 | -0.09 | 0.8150 | 0.0083731 |
| 37383568 | EIF2AK2 | 0.09 | 0.8260 | 0.0073508 |
| 312419 | IFITM1 | -0.04 | 0.8400 | 0.0019811 |
| 312434 | IFITM1 | -0.01 | 0.9510 | 0.0001820 |
4.3.2 Figure22: The correlation between expression and methylation in CD4+ T cells
4.4 Correlation between gene expression and methylation in CD8+ T cells
4.4.1 Table 25: The correlation between expression and methylation in CD8+ T cells
| CpGs | Gene | Corr | Corr.p | Lm.r2 |
|---|---|---|---|---|
| 79085586 | IFI44L | -0.37 | 0.0383 | 0.1353133 |
| 79085765 | IFI44L | -0.36 | 0.0446 | 0.1277101 |
| 79085647 | IFI44L | -0.33 | 0.0620 | 0.1112939 |
| 42798747 | MX1 | -0.28 | 0.1030 | 0.0784902 |
| 122281939 | PARP9 | -0.29 | 0.1030 | 0.0863589 |
| 79085713 | IFI44L | -0.29 | 0.1130 | 0.0816564 |
| 42798723 | MX1 | -0.26 | 0.1310 | 0.0678477 |
| 37383730 | EIF2AK2 | -0.55 | 0.1600 | 0.3004069 |
| 122281975 | PARP9 | -0.25 | 0.1700 | 0.0619500 |
| 42798698 | MX1 | -0.23 | 0.1760 | 0.0546541 |
| 312463 | IFITM1 | -0.26 | 0.1850 | 0.0691613 |
| 42798781 | MX1 | -0.21 | 0.2360 | 0.0423371 |
| 42798695 | MX1 | -0.17 | 0.3250 | 0.0293229 |
| 312434 | IFITM1 | -0.19 | 0.3710 | 0.0349896 |
| 37383568 | EIF2AK2 | 0.34 | 0.4130 | 0.1143366 |
| 42798863 | MX1 | -0.13 | 0.4500 | 0.0173745 |
| 42798813 | MX1 | -0.13 | 0.4530 | 0.0171822 |
| 312419 | IFITM1 | -0.15 | 0.4700 | 0.0229366 |
| 42798837 | MX1 | -0.12 | 0.4800 | 0.0151987 |
| 42798829 | MX1 | -0.12 | 0.4850 | 0.0149143 |
| 42798765 | MX1 | -0.12 | 0.4890 | 0.0145876 |
| 42798857 | MX1 | -0.11 | 0.5310 | 0.0119887 |
| 37383713 | EIF2AK2 | -0.26 | 0.5310 | 0.0686151 |
| 42798816 | MX1 | -0.11 | 0.5390 | 0.0115668 |
| 42798847 | MX1 | -0.11 | 0.5440 | 0.0112528 |
| 37383588 | EIF2AK2 | 0.25 | 0.5500 | 0.0626145 |
| 37383623 | EIF2AK2 | 0.23 | 0.5800 | 0.0540205 |
| 42798818 | MX1 | -0.09 | 0.5880 | 0.0089814 |
| 42798733 | MX1 | -0.09 | 0.6230 | 0.0074243 |
| 313408 | IFITM1 | -0.08 | 0.6540 | 0.0061667 |
| 42798749 | MX1 | -0.07 | 0.6700 | 0.0055590 |
| 312518 | IFITM1 | -0.10 | 0.7200 | 0.0094701 |
| 313354 | IFITM1 | 0.05 | 0.7580 | 0.0029280 |
| 37383679 | EIF2AK2 | -0.05 | 0.9080 | 0.0024280 |
4.4.2 Figure23: The correlation between expression and methylation in CD8+ T cells
4.5 Correlation between gene expression and methylation in CD4+ and CD8+ T cells
4.5.1 Table26: The correlation between expression and methylation in CD4+ and CD8+ T cells
| CpGs | Gene | Corr | Corr.p | Lm.r2 |
|---|---|---|---|---|
| 79085586 | IFI44L | -0.32 | 0.0114 | 0.1018940 |
| 79085765 | IFI44L | -0.28 | 0.0257 | 0.0802068 |
| 79085713 | IFI44L | -0.27 | 0.0353 | 0.0717273 |
| 122281975 | PARP9 | -0.24 | 0.0602 | 0.0566870 |
| 122281939 | PARP9 | -0.24 | 0.0635 | 0.0553203 |
| 42798747 | MX1 | -0.23 | 0.0656 | 0.0519690 |
| 79085647 | IFI44L | -0.23 | 0.0782 | 0.0508008 |
| 42798723 | MX1 | -0.21 | 0.0893 | 0.0444426 |
| 42798698 | MX1 | -0.18 | 0.1440 | 0.0330772 |
| 42798781 | MX1 | -0.14 | 0.2670 | 0.0191954 |
| 42798695 | MX1 | -0.14 | 0.2710 | 0.0188882 |
| 312463 | IFITM1 | 0.13 | 0.3350 | 0.0175711 |
| 37383588 | EIF2AK2 | -0.24 | 0.3440 | 0.0598388 |
| 42798863 | MX1 | -0.11 | 0.3830 | 0.0119045 |
| 312419 | IFITM1 | -0.12 | 0.4110 | 0.0147693 |
| 42798857 | MX1 | -0.10 | 0.4120 | 0.0105492 |
| 42798765 | MX1 | -0.10 | 0.4170 | 0.0103252 |
| 42798829 | MX1 | -0.09 | 0.4480 | 0.0090064 |
| 42798837 | MX1 | -0.09 | 0.4690 | 0.0082269 |
| 42798816 | MX1 | -0.09 | 0.4780 | 0.0078791 |
| 42798813 | MX1 | -0.08 | 0.5140 | 0.0066742 |
| 42798847 | MX1 | -0.08 | 0.5140 | 0.0066985 |
| 42798749 | MX1 | -0.08 | 0.5460 | 0.0057101 |
| 42798818 | MX1 | -0.07 | 0.5680 | 0.0051275 |
| 42798733 | MX1 | -0.07 | 0.5760 | 0.0049210 |
| 37383713 | EIF2AK2 | 0.12 | 0.6440 | 0.0145916 |
| 37383679 | EIF2AK2 | 0.10 | 0.7090 | 0.0095426 |
| 312434 | IFITM1 | -0.05 | 0.7520 | 0.0021864 |
| 37383623 | EIF2AK2 | -0.08 | 0.7550 | 0.0066994 |
| 312518 | IFITM1 | 0.05 | 0.7970 | 0.0024817 |
| 313408 | IFITM1 | 0.03 | 0.8080 | 0.0009252 |
| 37383568 | EIF2AK2 | 0.06 | 0.8100 | 0.0039840 |
| 37383730 | EIF2AK2 | -0.06 | 0.8270 | 0.0033006 |
| 313354 | IFITM1 | 0.00 | 0.9970 | 0.0000002 |
4.5.2 Figure24: The correlation between expression and methylation in CD4+ and CD8+ T cells
4.6 PartIII Summary:
In this part, we conducted the differential expression analysis between the SSc patients and Controls in both CD4+ and CD8+ T cells. And we found that nearly all of the genes showing differential methylation status in CD4+ and CD8+ T cells. However, due to the limited sample sizes, we found some of them showed marginal p-value which needs further confirmation with larger sample size. And In the correlation analysis between DNA methylation and expression, we only found the IFI44L gene showing significant negative correlation between methylation and expression. And we also found the other genes also showing negative correlation though the p-value of the correlation is not significant. And we believe that the limited sample sizes may be the main cause of it and further experiments are needed for convince it. In conclusion, with the above datasets, we still believe that the methylation and expression changes in the type I IFN related genes were negative and consistent, and the decreased methylation in SSc patients leads to the higher expression of these genes in CD4+ and CD8+ T cells, thus may induce further biological changes and might be associated with SSc pathogenesis.
5 Part IV: Differential serum type I IFN level and its correlation with gene expression and methylation
5.1 Figure 25: Differential serum type I IFN alpha level between SSc patients and Controls
[1] "The Mean Type I IFN alpha level in SSc is 25.174362, and The Mean Type I IFN alpha level in Control is 14.424465, the p-value between cases and controls conducted with wilcox signed rank test is 0.00000064"
[1] "Plot the Expression status of type I IFN alpha"
5.2 Figure 26: Differential serum type I IFN beta level between SSc patients and Controls
[1] "The Mean Type I IFN beta level in SSc is 91.090179, and The Mean Type I IFN beta level in Control is 40.276884, the p-value between cases and controls conducted with wilcox signed rank test is 0.00203729"
[1] "Plot the Expression status of type I IFN beta"
5.3 Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells
5.3.1 Table 27: Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells
| Genes | Corr | Corr.p | Lm.r2 |
|---|---|---|---|
| IFITM1 | 0.32 | 0.0315 | 0.1054195 |
| IFI44L | 0.30 | 0.0518 | 0.0870987 |
| PARP9 | 0.23 | 0.1380 | 0.0515756 |
| MX1 | 0.13 | 0.4130 | 0.0160291 |
| EIF2AK2 | 0.19 | 0.4230 | 0.0359393 |
5.3.2 Figure27: Correlation of serum type I IFN alpha level and gene expression in CD4+ T cells
5.4 Correlation of serum type I IFN beta level and gene expression in CD4+ T cells
5.4.1 Table 28: Correlation of serum type I IFN beta level and gene expression in CD4+ T cells
| Genes | Corr | Corr.p | Lm.r2 |
|---|---|---|---|
| IFITM1 | 0.46 | 0.00165 | 0.2121877 |
| EIF2AK2 | 0.61 | 0.00452 | 0.3687833 |
| PARP9 | 0.42 | 0.00497 | 0.1731270 |
| MX1 | 0.25 | 0.09790 | 0.0638792 |
| IFI44L | 0.10 | 0.50000 | 0.0109112 |
5.4.2 Figure28: Correlation of serum type I IFN beta level and gene expression in CD4+ T cells
5.5 Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells
5.5.1 Table 29: Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells
| Genes | Corr | Corr.p | Lm.r2 |
|---|---|---|---|
| EIF2AK2 | -0.41 | 0.0690 | 0.1720944 |
| IFI44L | 0.26 | 0.0804 | 0.0693922 |
| MX1 | 0.25 | 0.0924 | 0.0644428 |
| IFITM1 | 0.17 | 0.2660 | 0.0287167 |
| PARP9 | 0.07 | 0.6680 | 0.0043210 |
5.5.2 Figure29: Correlation of serum type I IFN alpha level and gene expression in CD8+ T cells
5.6 Correlation of serum type I IFN beta level and gene expression in CD8+ T cells
5.6.1 Table 30: Correlation of serum type I IFN beta level and gene expression in CD8+ T cells
| Genes | Corr | Corr.p | Lm.r2 |
|---|---|---|---|
| IFITM1 | 0.24 | 0.106 | 0.0596911 |
| PARP9 | 0.19 | 0.201 | 0.0377456 |
| MX1 | 0.19 | 0.206 | 0.0368811 |
| IFI44L | 0.06 | 0.707 | 0.0033088 |
| EIF2AK2 | 0.07 | 0.773 | 0.0047385 |
5.6.2 Figure30: Correlation of serum type I IFN beta level and gene expression in CD8+ T cells
5.7 Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
5.7.1 Table 31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
| CpGs | CpGnames | Gene | Corr.alpha | P.value | FDR | |
|---|---|---|---|---|---|---|
| 112 | 62199181 | cg06064964 | HELZ2 | 0.45 | 0.000429 | 0.0701575 |
| 84 | 313354 | cg11694510 | IFITM1 | -0.41 | 0.000665 | 0.0701575 |
| 104 | 122281975 | cg00959259 | PARP9 | -0.38 | 0.002060 | 0.1448867 |
| 103 | 122281939 | cg08122652 | PARP9 | -0.33 | 0.008120 | 0.4283300 |
| 114 | 37383568 | cg17326313 | EIF2AK2 | -0.31 | 0.012800 | 0.5244857 |
| 208 | 79085713 | cg17980508 | IFI44L | -0.30 | 0.015600 | 0.5244857 |
| 206 | 79085586 | cg03607951 | IFI44L | -0.30 | 0.017400 | 0.5244857 |
| 16 | 42798863 | Not In Discovery | MX1 | -0.26 | 0.039500 | 0.8419314 |
| 15 | 42798857 | Not In Discovery | MX1 | -0.26 | 0.040200 | 0.8419314 |
| 14 | 42798847 | Not In Discovery | MX1 | -0.25 | 0.044300 | 0.8419314 |
| 12 | 42798829 | Not In Discovery | MX1 | -0.25 | 0.047400 | 0.8419314 |
| 10 | 42798816 | Not In Discovery | MX1 | -0.24 | 0.052100 | 0.8419314 |
| 115 | 37383588 | Not In Discovery | EIF2AK2 | -0.24 | 0.052100 | 0.8419314 |
| 207 | 79085647 | Not In Discovery | IFI44L | -0.24 | 0.059100 | 0.8419314 |
| 209 | 79085765 | cg00855901 | IFI44L | -0.23 | 0.064300 | 0.8419314 |
| 5 | 42798747 | cg08924203 | MX1 | -0.23 | 0.069800 | 0.8419314 |
| 3 | 42798723 | Not In Discovery | MX1 | -0.22 | 0.075700 | 0.8419314 |
| 85 | 313408 | Not In Discovery | IFITM1 | -0.22 | 0.077700 | 0.8419314 |
| 180 | 1178105 | Not In Discovery | FAM132A | -0.22 | 0.079300 | 0.8419314 |
| 49 | 76145702 | Not In Discovery | UPK3B | -0.21 | 0.091100 | 0.8419314 |
| 13 | 42798837 | Not In Discovery | MX1 | -0.21 | 0.092800 | 0.8419314 |
| 22 | 67361798 | Not In Discovery | SMAD3 | 0.21 | 0.095700 | 0.8419314 |
| 57 | 76145589 | Not In Discovery | UPK3B | 0.20 | 0.103000 | 0.8419314 |
| 95 | 92414661 | Not In Discovery | BRDT | -0.20 | 0.108000 | 0.8419314 |
| 178 | 1178136 | Not In Discovery | FAM132A | -0.20 | 0.115000 | 0.8419314 |
| 2 | 42798698 | Not In Discovery | MX1 | -0.20 | 0.117000 | 0.8419314 |
| 100 | 92414770 | Not In Discovery | BRDT | -0.20 | 0.119000 | 0.8419314 |
| 185 | 33048423 | Not In Discovery | HLA-DPB1 | -0.20 | 0.123000 | 0.8419314 |
| 97 | 92414722 | cg14732540 | BRDT | -0.19 | 0.129000 | 0.8419314 |
| 130 | 38805839 | Not In Discovery | TLR1 | -0.20 | 0.129000 | 0.8419314 |
| 11 | 42798818 | Not In Discovery | MX1 | -0.19 | 0.131000 | 0.8419314 |
| 184 | 33048417 | Not In Discovery | HLA-DPB1 | -0.19 | 0.134000 | 0.8419314 |
| 101 | 92414782 | cg02935097 | BRDT | -0.19 | 0.135000 | 0.8419314 |
| 110 | 62199061 | Not In Discovery | HELZ2 | 0.20 | 0.138000 | 0.8419314 |
| 6 | 42798749 | Not In Discovery | MX1 | -0.18 | 0.153000 | 0.8419314 |
| 188 | 33048469 | cg10850215 | HLA-DPB1 | -0.18 | 0.162000 | 0.8419314 |
| 9 | 42798813 | Not In Discovery | MX1 | -0.17 | 0.164000 | 0.8419314 |
| 186 | 33048433 | Not In Discovery | HLA-DPB1 | -0.18 | 0.169000 | 0.8419314 |
| 21 | 67361773 | cg24961286 | SMAD3 | 0.17 | 0.177000 | 0.8419314 |
| 197 | 33048555 | cg19990651 | HLA-DPB1 | -0.17 | 0.181000 | 0.8419314 |
| 99 | 92414751 | Not In Discovery | BRDT | -0.17 | 0.190000 | 0.8419314 |
| 177 | 1178150 | Not In Discovery | FAM132A | -0.17 | 0.190000 | 0.8419314 |
| 191 | 33048502 | cg26645432 | HLA-DPB1 | -0.17 | 0.193000 | 0.8419314 |
| 199 | 33048571 | Not In Discovery | HLA-DPB1 | -0.16 | 0.202000 | 0.8419314 |
| 203 | 33048602 | Not In Discovery | HLA-DPB1 | -0.16 | 0.202000 | 0.8419314 |
| 102 | 92414793 | Not In Discovery | BRDT | -0.16 | 0.210000 | 0.8419314 |
| 113 | 62199190 | cg09844573 | HELZ2 | 0.17 | 0.212000 | 0.8419314 |
| 111 | 62199156 | cg11779113 | HELZ2 | 0.17 | 0.218000 | 0.8419314 |
| 23 | 67361821 | Not In Discovery | SMAD3 | 0.16 | 0.219000 | 0.8419314 |
| 176 | 1178162 | Not In Discovery | FAM132A | -0.16 | 0.219000 | 0.8419314 |
| 1 | 42798695 | Not In Discovery | MX1 | -0.15 | 0.227000 | 0.8419314 |
| 174 | 1178182 | Not In Discovery | FAM132A | -0.15 | 0.230000 | 0.8419314 |
| 44 | 30039208 | Not In Discovery | RNF39 | 0.15 | 0.236000 | 0.8419314 |
| 19 | 33048310 | cg13349035 | HLA-DPB1 | -0.15 | 0.249000 | 0.8419314 |
| 198 | 33048558 | cg01132696 | HLA-DPB1 | -0.15 | 0.251000 | 0.8419314 |
| 202 | 33048592 | Not In Discovery | HLA-DPB1 | -0.14 | 0.261000 | 0.8419314 |
| 200 | 33048575 | Not In Discovery | HLA-DPB1 | -0.14 | 0.262000 | 0.8419314 |
| 42 | 30039202 | Not In Discovery | RNF39 | 0.14 | 0.269000 | 0.8419314 |
| 51 | 76145689 | Not In Discovery | UPK3B | -0.14 | 0.271000 | 0.8419314 |
| 187 | 33048444 | Not In Discovery | HLA-DPB1 | -0.14 | 0.278000 | 0.8419314 |
| 17 | 33048286 | cg09234582 | HLA-DPB1 | -0.14 | 0.285000 | 0.8419314 |
| 18 | 33048291 | cg25045942 | HLA-DPB1 | -0.13 | 0.296000 | 0.8419314 |
| 190 | 33048485 | cg17588455 | HLA-DPB1 | -0.13 | 0.297000 | 0.8419314 |
| 118 | 37383713 | Not In Discovery | EIF2AK2 | -0.13 | 0.301000 | 0.8419314 |
| 193 | 33048540 | cg14870156 | HLA-DPB1 | -0.13 | 0.303000 | 0.8419314 |
| 195 | 33048544 | Not In Discovery | HLA-DPB1 | -0.13 | 0.310000 | 0.8419314 |
| 196 | 33048549 | Not In Discovery | HLA-DPB1 | -0.13 | 0.310000 | 0.8419314 |
| 98 | 92414737 | cg13299824 | BRDT | -0.13 | 0.311000 | 0.8419314 |
| 201 | 33048581 | Not In Discovery | HLA-DPB1 | -0.13 | 0.320000 | 0.8419314 |
| 183 | 92418017 | Not In Discovery | BRDT | -0.12 | 0.325000 | 0.8419314 |
| 37 | 30039142 | cg00947782 | RNF39 | 0.12 | 0.334000 | 0.8419314 |
| 8 | 42798781 | Not In Discovery | MX1 | -0.12 | 0.344000 | 0.8419314 |
| 205 | 312463 | Not In Discovery | IFITM1 | -0.13 | 0.347000 | 0.8419314 |
| 96 | 92414719 | Not In Discovery | BRDT | -0.12 | 0.351000 | 0.8419314 |
| 92 | 12877235 | Not In Discovery | HOOK2 | -0.12 | 0.357000 | 0.8419314 |
| 131 | 12877020 | Not In Discovery | HOOK2 | -0.12 | 0.358000 | 0.8419314 |
| 144 | 12876911 | Not In Discovery | HOOK2 | -0.12 | 0.361000 | 0.8419314 |
| 132 | 12877001 | cg11738485 | HOOK2 | -0.12 | 0.362000 | 0.8419314 |
| 135 | 12876987 | Not In Discovery | HOOK2 | -0.12 | 0.362000 | 0.8419314 |
| 140 | 12876942 | Not In Discovery | HOOK2 | -0.11 | 0.362000 | 0.8419314 |
| 139 | 12876944 | Not In Discovery | HOOK2 | -0.11 | 0.363000 | 0.8419314 |
| 143 | 12876918 | Not In Discovery | HOOK2 | -0.11 | 0.365000 | 0.8419314 |
| 43 | 30039206 | Not In Discovery | RNF39 | 0.11 | 0.366000 | 0.8419314 |
| 93 | 12877276 | Not In Discovery | HOOK2 | -0.11 | 0.366000 | 0.8419314 |
| 137 | 12876948 | Not In Discovery | HOOK2 | -0.11 | 0.367000 | 0.8419314 |
| 138 | 12876946 | Not In Discovery | HOOK2 | -0.11 | 0.371000 | 0.8419314 |
| 192 | 33048529 | cg06437840 | HLA-DPB1 | -0.11 | 0.372000 | 0.8419314 |
| 91 | 12877215 | Not In Discovery | HOOK2 | -0.11 | 0.374000 | 0.8419314 |
| 134 | 12876993 | Not In Discovery | HOOK2 | -0.11 | 0.375000 | 0.8419314 |
| 142 | 12876926 | Not In Discovery | HOOK2 | -0.11 | 0.375000 | 0.8419314 |
| 88 | 12877138 | Not In Discovery | HOOK2 | -0.11 | 0.376000 | 0.8419314 |
| 136 | 12876969 | Not In Discovery | HOOK2 | -0.11 | 0.376000 | 0.8419314 |
| 179 | 1178118 | Not In Discovery | FAM132A | 0.11 | 0.376000 | 0.8419314 |
| 141 | 12876937 | Not In Discovery | HOOK2 | -0.11 | 0.377000 | 0.8419314 |
| 133 | 12876997 | Not In Discovery | HOOK2 | -0.11 | 0.383000 | 0.8419314 |
| 106 | 75954053 | cg25716013 | COX7A2 | -0.11 | 0.390000 | 0.8419314 |
| 86 | 12877099 | Not In Discovery | HOOK2 | -0.11 | 0.393000 | 0.8419314 |
| 39 | 30039158 | Not In Discovery | RNF39 | 0.11 | 0.394000 | 0.8419314 |
| 56 | 76145606 | Not In Discovery | UPK3B | 0.11 | 0.402000 | 0.8419314 |
| 87 | 12877107 | Not In Discovery | HOOK2 | -0.11 | 0.404000 | 0.8419314 |
| 211 | 312518 | cg05432003 | IFITM1 | -0.17 | 0.405000 | 0.8419314 |
| 90 | 12877201 | Not In Discovery | HOOK2 | -0.10 | 0.407000 | 0.8419314 |
| 189 | 33048483 | cg03229061 | HLA-DPB1 | -0.10 | 0.423000 | 0.8665340 |
| 46 | 30039235 | Not In Discovery | RNF39 | 0.10 | 0.443000 | 0.8987788 |
| 94 | 92414650 | Not In Discovery | BRDT | -0.10 | 0.453000 | 0.9103143 |
| 89 | 12877188 | cg23899408 | HOOK2 | -0.09 | 0.458000 | 0.9116792 |
| 83 | 21572623 | cg12639429 | TTC39C | -0.09 | 0.464000 | 0.9149907 |
| 82 | 21572635 | cg05401069 | TTC39C | -0.09 | 0.469000 | 0.9162870 |
| 4 | 42798733 | Not In Discovery | MX1 | -0.09 | 0.482000 | 0.9284000 |
| 41 | 30039186 | Not In Discovery | RNF39 | 0.09 | 0.484000 | 0.9284000 |
| 182 | 92417998 | cg01081438 | BRDT | 0.08 | 0.510000 | 0.9393313 |
| 28 | 75953883 | Not In Discovery | COX7A2 | -0.08 | 0.512000 | 0.9393313 |
| 45 | 30039232 | Not In Discovery | RNF39 | 0.08 | 0.531000 | 0.9393313 |
| 204 | 312434 | Not In Discovery | IFITM1 | -0.09 | 0.540000 | 0.9393313 |
| 123 | 179741081 | Not In Discovery | GFPT2 | 0.08 | 0.553000 | 0.9393313 |
| 122 | 179741101 | Not In Discovery | GFPT2 | 0.07 | 0.582000 | 0.9393313 |
| 128 | 179741039 | Not In Discovery | GFPT2 | 0.07 | 0.586000 | 0.9393313 |
| 149 | 179740970 | Not In Discovery | GFPT2 | 0.07 | 0.590000 | 0.9393313 |
| 127 | 179741042 | Not In Discovery | GFPT2 | 0.07 | 0.591000 | 0.9393313 |
| 79 | 30039466 | cg16078649 | RNF39 | -0.07 | 0.598000 | 0.9393313 |
| 31 | 75953960 | Not In Discovery | COX7A2 | -0.07 | 0.603000 | 0.9393313 |
| 175 | 1178172 | Not In Discovery | FAM132A | -0.07 | 0.603000 | 0.9393313 |
| 73 | 30039411 | Not In Discovery | RNF39 | 0.07 | 0.609000 | 0.9393313 |
| 54 | 76145628 | Not In Discovery | UPK3B | -0.06 | 0.614000 | 0.9393313 |
| 36 | 30039132 | Not In Discovery | RNF39 | 0.06 | 0.616000 | 0.9393313 |
| 76 | 30039432 | cg13401893 | RNF39 | -0.06 | 0.619000 | 0.9393313 |
| 105 | 75954022 | Not In Discovery | COX7A2 | -0.06 | 0.620000 | 0.9393313 |
| 124 | 179741067 | Not In Discovery | GFPT2 | 0.06 | 0.621000 | 0.9393313 |
| 32 | 75953974 | Not In Discovery | COX7A2 | -0.06 | 0.622000 | 0.9393313 |
| 147 | 179740994 | Not In Discovery | GFPT2 | 0.06 | 0.624000 | 0.9393313 |
| 150 | 179740963 | Not In Discovery | GFPT2 | 0.06 | 0.629000 | 0.9393313 |
| 155 | 179740920 | Not In Discovery | GFPT2 | 0.06 | 0.630000 | 0.9393313 |
| 159 | 179740900 | Not In Discovery | GFPT2 | 0.06 | 0.630000 | 0.9393313 |
| 153 | 179740940 | Not In Discovery | GFPT2 | 0.06 | 0.635000 | 0.9393313 |
| 126 | 179741060 | Not In Discovery | GFPT2 | 0.06 | 0.636000 | 0.9393313 |
| 30 | 75953937 | Not In Discovery | COX7A2 | -0.06 | 0.640000 | 0.9393313 |
| 151 | 179740957 | Not In Discovery | GFPT2 | 0.06 | 0.647000 | 0.9393313 |
| 154 | 179740935 | Not In Discovery | GFPT2 | 0.06 | 0.648000 | 0.9393313 |
| 152 | 179740955 | Not In Discovery | GFPT2 | 0.06 | 0.650000 | 0.9393313 |
| 156 | 179740918 | Not In Discovery | GFPT2 | 0.06 | 0.651000 | 0.9393313 |
| 146 | 179740999 | Not In Discovery | GFPT2 | 0.06 | 0.657000 | 0.9393313 |
| 40 | 30039175 | cg03343571 | RNF39 | 0.06 | 0.661000 | 0.9393313 |
| 158 | 179740906 | Not In Discovery | GFPT2 | 0.06 | 0.662000 | 0.9393313 |
| 145 | 179741008 | Not In Discovery | GFPT2 | 0.05 | 0.663000 | 0.9393313 |
| 117 | 37383679 | Not In Discovery | EIF2AK2 | 0.05 | 0.666000 | 0.9393313 |
| 125 | 179741063 | Not In Discovery | GFPT2 | 0.05 | 0.669000 | 0.9393313 |
| 148 | 179740992 | Not In Discovery | GFPT2 | 0.05 | 0.669000 | 0.9393313 |
| 38 | 30039151 | cg18930910 | RNF39 | 0.05 | 0.680000 | 0.9393313 |
| 157 | 179740915 | cg13944838 | GFPT2 | 0.05 | 0.682000 | 0.9393313 |
| 48 | 76145717 | Not In Discovery | UPK3B | -0.05 | 0.688000 | 0.9393313 |
| 160 | 179740888 | Not In Discovery | GFPT2 | 0.05 | 0.688000 | 0.9393313 |
| 58 | 30039271 | Not In Discovery | RNF39 | -0.05 | 0.693000 | 0.9393313 |
| 121 | 179741105 | cg23248424 | GFPT2 | 0.05 | 0.693000 | 0.9393313 |
| 129 | 38805732 | cg02016764 | TLR1 | 0.05 | 0.693000 | 0.9393313 |
| 52 | 76145673 | cg05372444 | UPK3B | -0.05 | 0.695000 | 0.9393313 |
| 66 | 30039354 | Not In Discovery | RNF39 | -0.05 | 0.703000 | 0.9393313 |
| 116 | 37383623 | Not In Discovery | EIF2AK2 | 0.05 | 0.704000 | 0.9393313 |
| 107 | 75954118 | Not In Discovery | COX7A2 | -0.05 | 0.710000 | 0.9393313 |
| 68 | 30039374 | cg20249327 | RNF39 | -0.05 | 0.717000 | 0.9393313 |
| 20 | 33048370 | Not In Discovery | HLA-DPB1 | -0.05 | 0.721000 | 0.9393313 |
| 108 | 75954122 | Not In Discovery | COX7A2 | -0.05 | 0.724000 | 0.9393313 |
| 210 | 312419 | Not In Discovery | IFITM1 | 0.05 | 0.727000 | 0.9393313 |
| 75 | 30039418 | Not In Discovery | RNF39 | -0.04 | 0.728000 | 0.9393313 |
| 120 | 179741121 | cg02891314 | GFPT2 | 0.04 | 0.733000 | 0.9393313 |
| 35 | 30039130 | Not In Discovery | RNF39 | -0.04 | 0.738000 | 0.9393313 |
| 69 | 30039376 | cg15877520 | RNF39 | -0.04 | 0.739000 | 0.9393313 |
| 109 | 62199034 | cg17593958 | HELZ2 | 0.04 | 0.748000 | 0.9429742 |
| 63 | 30039313 | Not In Discovery | RNF39 | -0.04 | 0.758000 | 0.9429742 |
| 78 | 30039442 | cg10568066 | RNF39 | -0.04 | 0.762000 | 0.9429742 |
| 7 | 42798765 | Not In Discovery | MX1 | -0.04 | 0.779000 | 0.9429742 |
| 172 | 1178202 | Not In Discovery | FAM132A | -0.04 | 0.779000 | 0.9429742 |
| 33 | 30039123 | Not In Discovery | RNF39 | 0.03 | 0.790000 | 0.9429742 |
| 119 | 37383730 | Not In Discovery | EIF2AK2 | -0.03 | 0.792000 | 0.9429742 |
| 81 | 21572657 | cg18719665 | TTC39C | -0.03 | 0.795000 | 0.9429742 |
| 166 | 179740840 | Not In Discovery | GFPT2 | 0.03 | 0.796000 | 0.9429742 |
| 71 | 30039403 | cg09279736 | RNF39 | -0.03 | 0.799000 | 0.9429742 |
| 168 | 179740825 | Not In Discovery | GFPT2 | 0.03 | 0.799000 | 0.9429742 |
| 26 | 75953829 | Not In Discovery | COX7A2 | -0.03 | 0.802000 | 0.9429742 |
| 161 | 179740869 | Not In Discovery | GFPT2 | 0.03 | 0.803000 | 0.9429742 |
| 24 | 67361896 | Not In Discovery | SMAD3 | 0.03 | 0.807000 | 0.9429742 |
| 62 | 30039307 | Not In Discovery | RNF39 | -0.03 | 0.811000 | 0.9429742 |
| 47 | 30039239 | Not In Discovery | RNF39 | 0.03 | 0.814000 | 0.9429742 |
| 163 | 179740861 | Not In Discovery | GFPT2 | 0.03 | 0.818000 | 0.9429742 |
| 25 | 75953821 | Not In Discovery | COX7A2 | 0.03 | 0.824000 | 0.9429742 |
| 162 | 179740867 | Not In Discovery | GFPT2 | 0.03 | 0.832000 | 0.9429742 |
| 53 | 76145633 | cg16453056 | UPK3B | -0.03 | 0.836000 | 0.9429742 |
| 164 | 179740855 | Not In Discovery | GFPT2 | 0.03 | 0.843000 | 0.9429742 |
| 165 | 179740852 | Not In Discovery | GFPT2 | 0.02 | 0.847000 | 0.9429742 |
| 167 | 179740832 | Not In Discovery | GFPT2 | 0.02 | 0.851000 | 0.9429742 |
| 29 | 75953935 | cg19367436 | COX7A2 | -0.02 | 0.853000 | 0.9429742 |
| 61 | 30039303 | Not In Discovery | RNF39 | -0.02 | 0.860000 | 0.9429742 |
| 50 | 76145693 | Not In Discovery | UPK3B | -0.02 | 0.863000 | 0.9429742 |
| 169 | 179740822 | Not In Discovery | GFPT2 | 0.02 | 0.863000 | 0.9429742 |
| 64 | 30039323 | Not In Discovery | RNF39 | -0.02 | 0.867000 | 0.9429742 |
| 72 | 30039408 | cg07382347 | RNF39 | -0.02 | 0.876000 | 0.9478769 |
| 55 | 76145620 | Not In Discovery | UPK3B | -0.02 | 0.891000 | 0.9526970 |
| 27 | 75953853 | cg06809298 | COX7A2 | -0.02 | 0.894000 | 0.9526970 |
| 70 | 30039380 | cg13918754 | RNF39 | -0.02 | 0.894000 | 0.9526970 |
| 60 | 30039278 | Not In Discovery | RNF39 | 0.01 | 0.924000 | 0.9790400 |
| 59 | 30039274 | Not In Discovery | RNF39 | -0.01 | 0.928000 | 0.9790400 |
| 74 | 30039415 | Not In Discovery | RNF39 | -0.01 | 0.938000 | 0.9819615 |
| 77 | 30039435 | cg12633154 | RNF39 | 0.01 | 0.951000 | 0.9819615 |
| 34 | 30039127 | Not In Discovery | RNF39 | 0.01 | 0.953000 | 0.9819615 |
| 171 | 1178207 | Not In Discovery | FAM132A | -0.01 | 0.953000 | 0.9819615 |
| 65 | 30039349 | Not In Discovery | RNF39 | -0.01 | 0.962000 | 0.9819615 |
| 67 | 30039364 | Not In Discovery | RNF39 | 0.01 | 0.964000 | 0.9819615 |
| 170 | 1178246 | cg24345856 | FAM132A | 0.01 | 0.967000 | 0.9819615 |
| 181 | 1178086 | Not In Discovery | FAM132A | -0.01 | 0.968000 | 0.9819615 |
| 80 | 30039476 | cg10930308 | RNF39 | 0.00 | 0.974000 | 0.9833206 |
| 173 | 1178192 | Not In Discovery | FAM132A | 0.00 | 0.992000 | 0.9967238 |
| 194 | 33048542 | Not In Discovery | HLA-DPB1 | 0.00 | 0.999000 | 0.9990000 |
5.7.2 Figure31:Correlation of serum type I IFN alpha level and gene methylation in CD4+ T cells
##Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells
5.7.3 Table 32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells
| CpGs | CpGnames | Gene | Corr.beta | P.value | FDR | |
|---|---|---|---|---|---|---|
| 85 | 313408 | Not In Discovery | IFITM1 | -0.40 | 0.000997 | 0.1696440 |
| 81 | 21572657 | cg18719665 | TTC39C | 0.38 | 0.002020 | 0.1696440 |
| 109 | 62199034 | cg17593958 | HELZ2 | 0.40 | 0.002530 | 0.1696440 |
| 112 | 62199181 | cg06064964 | HELZ2 | 0.38 | 0.003710 | 0.1696440 |
| 82 | 21572635 | cg05401069 | TTC39C | 0.35 | 0.004020 | 0.1696440 |
| 83 | 21572623 | cg12639429 | TTC39C | 0.34 | 0.006060 | 0.1923114 |
| 115 | 37383588 | Not In Discovery | EIF2AK2 | -0.34 | 0.006380 | 0.1923114 |
| 110 | 62199061 | Not In Discovery | HELZ2 | 0.32 | 0.015500 | 0.4032444 |
| 47 | 30039239 | Not In Discovery | RNF39 | 0.30 | 0.017200 | 0.4032444 |
| 51 | 76145689 | Not In Discovery | UPK3B | -0.28 | 0.025900 | 0.5275000 |
| 84 | 313354 | cg11694510 | IFITM1 | -0.28 | 0.027500 | 0.5275000 |
| 104 | 122281975 | cg00959259 | PARP9 | -0.25 | 0.047200 | 0.7884737 |
| 43 | 30039206 | Not In Discovery | RNF39 | 0.25 | 0.050800 | 0.7884737 |
| 103 | 122281939 | cg08122652 | PARP9 | -0.24 | 0.055900 | 0.7884737 |
| 52 | 76145673 | cg05372444 | UPK3B | -0.23 | 0.062100 | 0.7884737 |
| 113 | 62199190 | cg09844573 | HELZ2 | 0.25 | 0.063500 | 0.7884737 |
| 114 | 37383568 | cg17326313 | EIF2AK2 | -0.23 | 0.066700 | 0.7884737 |
| 27 | 75953853 | cg06809298 | COX7A2 | -0.22 | 0.080600 | 0.7884737 |
| 25 | 75953821 | Not In Discovery | COX7A2 | -0.22 | 0.083200 | 0.7884737 |
| 42 | 30039202 | Not In Discovery | RNF39 | 0.22 | 0.087400 | 0.7884737 |
| 15 | 42798857 | Not In Discovery | MX1 | -0.21 | 0.091800 | 0.7884737 |
| 22 | 67361798 | Not In Discovery | SMAD3 | 0.21 | 0.097800 | 0.7884737 |
| 32 | 75953974 | Not In Discovery | COX7A2 | -0.21 | 0.099100 | 0.7884737 |
| 16 | 42798863 | Not In Discovery | MX1 | -0.21 | 0.100000 | 0.7884737 |
| 41 | 30039186 | Not In Discovery | RNF39 | 0.21 | 0.101000 | 0.7884737 |
| 46 | 30039235 | Not In Discovery | RNF39 | 0.21 | 0.103000 | 0.7884737 |
| 12 | 42798829 | Not In Discovery | MX1 | -0.20 | 0.105000 | 0.7884737 |
| 28 | 75953883 | Not In Discovery | COX7A2 | -0.21 | 0.109000 | 0.7884737 |
| 67 | 30039364 | Not In Discovery | RNF39 | 0.20 | 0.114000 | 0.7884737 |
| 173 | 1178192 | Not In Discovery | FAM132A | -0.20 | 0.122000 | 0.7884737 |
| 182 | 92417998 | cg01081438 | BRDT | 0.19 | 0.122000 | 0.7884737 |
| 35 | 30039130 | Not In Discovery | RNF39 | 0.19 | 0.132000 | 0.7884737 |
| 40 | 30039175 | cg03343571 | RNF39 | 0.19 | 0.133000 | 0.7884737 |
| 203 | 33048602 | Not In Discovery | HLA-DPB1 | -0.19 | 0.133000 | 0.7884737 |
| 26 | 75953829 | Not In Discovery | COX7A2 | -0.19 | 0.135000 | 0.7884737 |
| 45 | 30039232 | Not In Discovery | RNF39 | 0.19 | 0.138000 | 0.7884737 |
| 33 | 30039123 | Not In Discovery | RNF39 | 0.19 | 0.140000 | 0.7884737 |
| 206 | 79085586 | cg03607951 | IFI44L | -0.19 | 0.142000 | 0.7884737 |
| 50 | 76145693 | Not In Discovery | UPK3B | -0.18 | 0.147000 | 0.7953077 |
| 14 | 42798847 | Not In Discovery | MX1 | -0.17 | 0.170000 | 0.8267755 |
| 3 | 42798723 | Not In Discovery | MX1 | -0.17 | 0.172000 | 0.8267755 |
| 21 | 67361773 | cg24961286 | SMAD3 | 0.17 | 0.176000 | 0.8267755 |
| 31 | 75953960 | Not In Discovery | COX7A2 | -0.17 | 0.191000 | 0.8267755 |
| 30 | 75953937 | Not In Discovery | COX7A2 | -0.16 | 0.203000 | 0.8267755 |
| 19 | 33048310 | cg13349035 | HLA-DPB1 | -0.16 | 0.206000 | 0.8267755 |
| 20 | 33048370 | Not In Discovery | HLA-DPB1 | -0.16 | 0.212000 | 0.8267755 |
| 106 | 75954053 | cg25716013 | COX7A2 | -0.16 | 0.212000 | 0.8267755 |
| 34 | 30039127 | Not In Discovery | RNF39 | 0.16 | 0.213000 | 0.8267755 |
| 11 | 42798818 | Not In Discovery | MX1 | -0.15 | 0.225000 | 0.8267755 |
| 208 | 79085713 | cg17980508 | IFI44L | -0.15 | 0.232000 | 0.8267755 |
| 170 | 1178246 | cg24345856 | FAM132A | 0.15 | 0.238000 | 0.8267755 |
| 130 | 38805839 | Not In Discovery | TLR1 | -0.15 | 0.249000 | 0.8267755 |
| 29 | 75953935 | cg19367436 | COX7A2 | -0.15 | 0.251000 | 0.8267755 |
| 10 | 42798816 | Not In Discovery | MX1 | -0.14 | 0.256000 | 0.8267755 |
| 105 | 75954022 | Not In Discovery | COX7A2 | -0.14 | 0.259000 | 0.8267755 |
| 119 | 37383730 | Not In Discovery | EIF2AK2 | -0.14 | 0.268000 | 0.8267755 |
| 9 | 42798813 | Not In Discovery | MX1 | -0.14 | 0.271000 | 0.8267755 |
| 156 | 179740918 | Not In Discovery | GFPT2 | -0.14 | 0.272000 | 0.8267755 |
| 44 | 30039208 | Not In Discovery | RNF39 | 0.14 | 0.277000 | 0.8267755 |
| 13 | 42798837 | Not In Discovery | MX1 | -0.14 | 0.278000 | 0.8267755 |
| 17 | 33048286 | cg09234582 | HLA-DPB1 | -0.14 | 0.281000 | 0.8267755 |
| 155 | 179740920 | Not In Discovery | GFPT2 | -0.14 | 0.281000 | 0.8267755 |
| 169 | 179740822 | Not In Discovery | GFPT2 | -0.14 | 0.281000 | 0.8267755 |
| 160 | 179740888 | Not In Discovery | GFPT2 | -0.13 | 0.293000 | 0.8267755 |
| 23 | 67361821 | Not In Discovery | SMAD3 | 0.13 | 0.296000 | 0.8267755 |
| 100 | 92414770 | Not In Discovery | BRDT | -0.13 | 0.307000 | 0.8267755 |
| 162 | 179740867 | Not In Discovery | GFPT2 | -0.13 | 0.309000 | 0.8267755 |
| 145 | 179741008 | Not In Discovery | GFPT2 | -0.13 | 0.311000 | 0.8267755 |
| 194 | 33048542 | Not In Discovery | HLA-DPB1 | 0.13 | 0.312000 | 0.8267755 |
| 175 | 1178172 | Not In Discovery | FAM132A | -0.13 | 0.314000 | 0.8267755 |
| 157 | 179740915 | cg13944838 | GFPT2 | -0.13 | 0.318000 | 0.8267755 |
| 7 | 42798765 | Not In Discovery | MX1 | -0.12 | 0.326000 | 0.8267755 |
| 158 | 179740906 | Not In Discovery | GFPT2 | -0.12 | 0.327000 | 0.8267755 |
| 57 | 76145589 | Not In Discovery | UPK3B | 0.12 | 0.328000 | 0.8267755 |
| 128 | 179741039 | Not In Discovery | GFPT2 | -0.12 | 0.331000 | 0.8267755 |
| 151 | 179740957 | Not In Discovery | GFPT2 | -0.12 | 0.332000 | 0.8267755 |
| 172 | 1178202 | Not In Discovery | FAM132A | -0.12 | 0.332000 | 0.8267755 |
| 107 | 75954118 | Not In Discovery | COX7A2 | -0.12 | 0.339000 | 0.8267755 |
| 102 | 92414793 | Not In Discovery | BRDT | -0.12 | 0.341000 | 0.8267755 |
| 154 | 179740935 | Not In Discovery | GFPT2 | -0.12 | 0.343000 | 0.8267755 |
| 149 | 179740970 | Not In Discovery | GFPT2 | -0.12 | 0.345000 | 0.8267755 |
| 181 | 1178086 | Not In Discovery | FAM132A | -0.12 | 0.346000 | 0.8267755 |
| 1 | 42798695 | Not In Discovery | MX1 | -0.12 | 0.352000 | 0.8267755 |
| 5 | 42798747 | cg08924203 | MX1 | -0.12 | 0.352000 | 0.8267755 |
| 153 | 179740940 | Not In Discovery | GFPT2 | -0.12 | 0.354000 | 0.8267755 |
| 146 | 179740999 | Not In Discovery | GFPT2 | -0.12 | 0.355000 | 0.8267755 |
| 159 | 179740900 | Not In Discovery | GFPT2 | -0.12 | 0.361000 | 0.8267755 |
| 152 | 179740955 | Not In Discovery | GFPT2 | -0.11 | 0.362000 | 0.8267755 |
| 127 | 179741042 | Not In Discovery | GFPT2 | -0.11 | 0.369000 | 0.8267755 |
| 165 | 179740852 | Not In Discovery | GFPT2 | -0.11 | 0.370000 | 0.8267755 |
| 147 | 179740994 | Not In Discovery | GFPT2 | -0.11 | 0.374000 | 0.8267755 |
| 167 | 179740832 | Not In Discovery | GFPT2 | -0.11 | 0.375000 | 0.8267755 |
| 108 | 75954122 | Not In Discovery | COX7A2 | -0.11 | 0.376000 | 0.8267755 |
| 210 | 312419 | Not In Discovery | IFITM1 | -0.13 | 0.378000 | 0.8267755 |
| 111 | 62199156 | cg11779113 | HELZ2 | 0.12 | 0.380000 | 0.8267755 |
| 148 | 179740992 | Not In Discovery | GFPT2 | -0.11 | 0.382000 | 0.8267755 |
| 150 | 179740963 | Not In Discovery | GFPT2 | -0.11 | 0.384000 | 0.8267755 |
| 163 | 179740861 | Not In Discovery | GFPT2 | -0.11 | 0.384000 | 0.8267755 |
| 18 | 33048291 | cg25045942 | HLA-DPB1 | -0.11 | 0.391000 | 0.8293762 |
| 166 | 179740840 | Not In Discovery | GFPT2 | -0.11 | 0.396000 | 0.8293762 |
| 204 | 312434 | Not In Discovery | IFITM1 | -0.13 | 0.397000 | 0.8293762 |
| 56 | 76145606 | Not In Discovery | UPK3B | -0.10 | 0.409000 | 0.8379135 |
| 171 | 1178207 | Not In Discovery | FAM132A | -0.10 | 0.410000 | 0.8379135 |
| 126 | 179741060 | Not In Discovery | GFPT2 | -0.10 | 0.413000 | 0.8379135 |
| 125 | 179741063 | Not In Discovery | GFPT2 | -0.10 | 0.419000 | 0.8415030 |
| 168 | 179740825 | Not In Discovery | GFPT2 | -0.10 | 0.424000 | 0.8415030 |
| 124 | 179741067 | Not In Discovery | GFPT2 | -0.10 | 0.430000 | 0.8415030 |
| 123 | 179741081 | Not In Discovery | GFPT2 | -0.10 | 0.438000 | 0.8415030 |
| 164 | 179740855 | Not In Discovery | GFPT2 | -0.10 | 0.441000 | 0.8415030 |
| 161 | 179740869 | Not In Discovery | GFPT2 | -0.09 | 0.461000 | 0.8415030 |
| 6 | 42798749 | Not In Discovery | MX1 | -0.09 | 0.468000 | 0.8415030 |
| 120 | 179741121 | cg02891314 | GFPT2 | -0.09 | 0.478000 | 0.8415030 |
| 39 | 30039158 | Not In Discovery | RNF39 | 0.09 | 0.486000 | 0.8415030 |
| 187 | 33048444 | Not In Discovery | HLA-DPB1 | -0.09 | 0.492000 | 0.8415030 |
| 8 | 42798781 | Not In Discovery | MX1 | -0.09 | 0.496000 | 0.8415030 |
| 121 | 179741105 | cg23248424 | GFPT2 | -0.09 | 0.504000 | 0.8415030 |
| 53 | 76145633 | cg16453056 | UPK3B | -0.08 | 0.512000 | 0.8415030 |
| 48 | 76145717 | Not In Discovery | UPK3B | -0.08 | 0.524000 | 0.8415030 |
| 122 | 179741101 | Not In Discovery | GFPT2 | -0.08 | 0.525000 | 0.8415030 |
| 198 | 33048558 | cg01132696 | HLA-DPB1 | -0.08 | 0.531000 | 0.8415030 |
| 117 | 37383679 | Not In Discovery | EIF2AK2 | 0.08 | 0.538000 | 0.8415030 |
| 72 | 30039408 | cg07382347 | RNF39 | -0.08 | 0.539000 | 0.8415030 |
| 202 | 33048592 | Not In Discovery | HLA-DPB1 | -0.08 | 0.540000 | 0.8415030 |
| 205 | 312463 | Not In Discovery | IFITM1 | -0.08 | 0.540000 | 0.8415030 |
| 207 | 79085647 | Not In Discovery | IFI44L | 0.08 | 0.544000 | 0.8415030 |
| 101 | 92414782 | cg02935097 | BRDT | -0.08 | 0.554000 | 0.8415030 |
| 180 | 1178105 | Not In Discovery | FAM132A | -0.07 | 0.556000 | 0.8415030 |
| 68 | 30039374 | cg20249327 | RNF39 | -0.07 | 0.557000 | 0.8415030 |
| 131 | 12877020 | Not In Discovery | HOOK2 | -0.07 | 0.568000 | 0.8415030 |
| 211 | 312518 | cg05432003 | IFITM1 | -0.12 | 0.574000 | 0.8415030 |
| 58 | 30039271 | Not In Discovery | RNF39 | -0.07 | 0.583000 | 0.8415030 |
| 199 | 33048571 | Not In Discovery | HLA-DPB1 | -0.07 | 0.583000 | 0.8415030 |
| 133 | 12876997 | Not In Discovery | HOOK2 | -0.07 | 0.589000 | 0.8415030 |
| 135 | 12876987 | Not In Discovery | HOOK2 | -0.07 | 0.592000 | 0.8415030 |
| 136 | 12876969 | Not In Discovery | HOOK2 | -0.07 | 0.592000 | 0.8415030 |
| 134 | 12876993 | Not In Discovery | HOOK2 | -0.07 | 0.595000 | 0.8415030 |
| 144 | 12876911 | Not In Discovery | HOOK2 | -0.07 | 0.596000 | 0.8415030 |
| 186 | 33048433 | Not In Discovery | HLA-DPB1 | -0.07 | 0.596000 | 0.8415030 |
| 174 | 1178182 | Not In Discovery | FAM132A | -0.07 | 0.597000 | 0.8415030 |
| 185 | 33048423 | Not In Discovery | HLA-DPB1 | -0.07 | 0.597000 | 0.8415030 |
| 137 | 12876948 | Not In Discovery | HOOK2 | -0.07 | 0.603000 | 0.8415030 |
| 139 | 12876944 | Not In Discovery | HOOK2 | -0.07 | 0.604000 | 0.8415030 |
| 141 | 12876937 | Not In Discovery | HOOK2 | -0.07 | 0.604000 | 0.8415030 |
| 24 | 67361896 | Not In Discovery | SMAD3 | 0.07 | 0.605000 | 0.8415030 |
| 140 | 12876942 | Not In Discovery | HOOK2 | -0.07 | 0.606000 | 0.8415030 |
| 132 | 12877001 | cg11738485 | HOOK2 | -0.07 | 0.607000 | 0.8415030 |
| 142 | 12876926 | Not In Discovery | HOOK2 | -0.06 | 0.608000 | 0.8415030 |
| 138 | 12876946 | Not In Discovery | HOOK2 | -0.06 | 0.610000 | 0.8415030 |
| 201 | 33048581 | Not In Discovery | HLA-DPB1 | -0.07 | 0.611000 | 0.8415030 |
| 80 | 30039476 | cg10930308 | RNF39 | -0.06 | 0.612000 | 0.8415030 |
| 183 | 92418017 | Not In Discovery | BRDT | -0.06 | 0.612000 | 0.8415030 |
| 143 | 12876918 | Not In Discovery | HOOK2 | -0.06 | 0.615000 | 0.8415030 |
| 89 | 12877188 | cg23899408 | HOOK2 | -0.06 | 0.619000 | 0.8415030 |
| 76 | 30039432 | cg13401893 | RNF39 | -0.06 | 0.622000 | 0.8415030 |
| 90 | 12877201 | Not In Discovery | HOOK2 | -0.06 | 0.625000 | 0.8415030 |
| 92 | 12877235 | Not In Discovery | HOOK2 | -0.06 | 0.625000 | 0.8415030 |
| 196 | 33048549 | Not In Discovery | HLA-DPB1 | -0.06 | 0.632000 | 0.8415030 |
| 91 | 12877215 | Not In Discovery | HOOK2 | -0.06 | 0.642000 | 0.8415030 |
| 184 | 33048417 | Not In Discovery | HLA-DPB1 | -0.06 | 0.642000 | 0.8415030 |
| 2 | 42798698 | Not In Discovery | MX1 | -0.06 | 0.643000 | 0.8415030 |
| 62 | 30039307 | Not In Discovery | RNF39 | -0.06 | 0.650000 | 0.8415030 |
| 129 | 38805732 | cg02016764 | TLR1 | 0.06 | 0.654000 | 0.8415030 |
| 87 | 12877107 | Not In Discovery | HOOK2 | -0.06 | 0.655000 | 0.8415030 |
| 94 | 92414650 | Not In Discovery | BRDT | -0.06 | 0.660000 | 0.8415030 |
| 75 | 30039418 | Not In Discovery | RNF39 | -0.06 | 0.661000 | 0.8415030 |
| 99 | 92414751 | Not In Discovery | BRDT | -0.05 | 0.668000 | 0.8415030 |
| 192 | 33048529 | cg06437840 | HLA-DPB1 | -0.05 | 0.669000 | 0.8415030 |
| 38 | 30039151 | cg18930910 | RNF39 | 0.05 | 0.673000 | 0.8415030 |
| 93 | 12877276 | Not In Discovery | HOOK2 | -0.05 | 0.674000 | 0.8415030 |
| 86 | 12877099 | Not In Discovery | HOOK2 | -0.05 | 0.678000 | 0.8415176 |
| 88 | 12877138 | Not In Discovery | HOOK2 | -0.05 | 0.687000 | 0.8477018 |
| 37 | 30039142 | cg00947782 | RNF39 | 0.05 | 0.696000 | 0.8488786 |
| 73 | 30039411 | Not In Discovery | RNF39 | 0.05 | 0.696000 | 0.8488786 |
| 61 | 30039303 | Not In Discovery | RNF39 | -0.05 | 0.704000 | 0.8537011 |
| 193 | 33048540 | cg14870156 | HLA-DPB1 | -0.05 | 0.720000 | 0.8681143 |
| 4 | 42798733 | Not In Discovery | MX1 | -0.04 | 0.729000 | 0.8739716 |
| 178 | 1178136 | Not In Discovery | FAM132A | -0.04 | 0.734000 | 0.8749944 |
| 191 | 33048502 | cg26645432 | HLA-DPB1 | -0.04 | 0.747000 | 0.8803011 |
| 195 | 33048544 | Not In Discovery | HLA-DPB1 | -0.04 | 0.756000 | 0.8803011 |
| 54 | 76145628 | Not In Discovery | UPK3B | -0.04 | 0.759000 | 0.8803011 |
| 209 | 79085765 | cg00855901 | IFI44L | -0.04 | 0.759000 | 0.8803011 |
| 69 | 30039376 | cg15877520 | RNF39 | -0.04 | 0.771000 | 0.8803011 |
| 60 | 30039278 | Not In Discovery | RNF39 | -0.04 | 0.774000 | 0.8803011 |
| 70 | 30039380 | cg13918754 | RNF39 | -0.04 | 0.775000 | 0.8803011 |
| 65 | 30039349 | Not In Discovery | RNF39 | -0.04 | 0.776000 | 0.8803011 |
| 79 | 30039466 | cg16078649 | RNF39 | -0.04 | 0.776000 | 0.8803011 |
| 55 | 76145620 | Not In Discovery | UPK3B | -0.03 | 0.787000 | 0.8880053 |
| 118 | 37383713 | Not In Discovery | EIF2AK2 | -0.03 | 0.806000 | 0.8995263 |
| 176 | 1178162 | Not In Discovery | FAM132A | 0.03 | 0.806000 | 0.8995263 |
| 197 | 33048555 | cg19990651 | HLA-DPB1 | -0.03 | 0.810000 | 0.8995263 |
| 189 | 33048483 | cg03229061 | HLA-DPB1 | 0.03 | 0.815000 | 0.9003403 |
| 188 | 33048469 | cg10850215 | HLA-DPB1 | -0.03 | 0.827000 | 0.9021327 |
| 95 | 92414661 | Not In Discovery | BRDT | -0.03 | 0.833000 | 0.9021327 |
| 36 | 30039132 | Not In Discovery | RNF39 | 0.03 | 0.835000 | 0.9021327 |
| 64 | 30039323 | Not In Discovery | RNF39 | -0.03 | 0.838000 | 0.9021327 |
| 200 | 33048575 | Not In Discovery | HLA-DPB1 | -0.03 | 0.838000 | 0.9021327 |
| 177 | 1178150 | Not In Discovery | FAM132A | 0.02 | 0.848000 | 0.9068737 |
| 74 | 30039415 | Not In Discovery | RNF39 | -0.02 | 0.851000 | 0.9068737 |
| 59 | 30039274 | Not In Discovery | RNF39 | -0.02 | 0.857000 | 0.9086784 |
| 179 | 1178118 | Not In Discovery | FAM132A | 0.02 | 0.866000 | 0.9136300 |
| 49 | 76145702 | Not In Discovery | UPK3B | 0.02 | 0.876000 | 0.9167586 |
| 78 | 30039442 | cg10568066 | RNF39 | -0.02 | 0.879000 | 0.9167586 |
| 66 | 30039354 | Not In Discovery | RNF39 | -0.02 | 0.882000 | 0.9167586 |
| 63 | 30039313 | Not In Discovery | RNF39 | -0.02 | 0.901000 | 0.9319167 |
| 190 | 33048485 | cg17588455 | HLA-DPB1 | -0.01 | 0.910000 | 0.9366341 |
| 98 | 92414737 | cg13299824 | BRDT | -0.01 | 0.918000 | 0.9402816 |
| 71 | 30039403 | cg09279736 | RNF39 | -0.01 | 0.949000 | 0.9673382 |
| 77 | 30039435 | cg12633154 | RNF39 | -0.01 | 0.957000 | 0.9708029 |
| 97 | 92414722 | cg14732540 | BRDT | 0.00 | 0.972000 | 0.9813014 |
| 96 | 92414719 | Not In Discovery | BRDT | 0.00 | 0.984000 | 0.9870000 |
| 116 | 37383623 | Not In Discovery | EIF2AK2 | 0.00 | 0.987000 | 0.9870000 |
5.7.4 Figure32:Correlation of serum type I IFN beta level and gene methylation in CD4+ T cells
5.8 Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells
5.8.1 Table 33:Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells
| CpGs | CpGnames | Gene | Corr.alpha | P.value | FDR | |
|---|---|---|---|---|---|---|
| 108 | 122281939 | cg08122652 | PARP9 | -0.38 | 0.00257 | 0.4272750 |
| 77 | 21572657 | cg18719665 | TTC39C | 0.35 | 0.00405 | 0.4272750 |
| 109 | 122281975 | cg00959259 | PARP9 | -0.34 | 0.00766 | 0.5387533 |
| 78 | 21572635 | cg05401069 | TTC39C | 0.32 | 0.01040 | 0.5486000 |
| 79 | 21572623 | cg12639429 | TTC39C | 0.29 | 0.01790 | 0.5886900 |
| 173 | 1178150 | Not In Discovery | FAM132A | -0.30 | 0.01840 | 0.5886900 |
| 103 | 62199034 | cg17593958 | HELZ2 | 0.31 | 0.02080 | 0.5886900 |
| 194 | 33048558 | cg01132696 | HLA-DPB1 | -0.30 | 0.02410 | 0.5886900 |
| 119 | 37383568 | cg17326313 | EIF2AK2 | -0.28 | 0.02690 | 0.5886900 |
| 6 | 42798749 | Not In Discovery | MX1 | -0.27 | 0.02790 | 0.5886900 |
| 196 | 33048575 | Not In Discovery | HLA-DPB1 | -0.27 | 0.03990 | 0.7284524 |
| 16 | 42798863 | Not In Discovery | MX1 | -0.25 | 0.04670 | 0.7284524 |
| 198 | 33048592 | Not In Discovery | HLA-DPB1 | -0.25 | 0.05460 | 0.7284524 |
| 192 | 33048549 | Not In Discovery | HLA-DPB1 | -0.24 | 0.06520 | 0.7284524 |
| 211 | 67361896 | Not In Discovery | SMAD3 | 0.24 | 0.06920 | 0.7284524 |
| 191 | 33048544 | Not In Discovery | HLA-DPB1 | -0.24 | 0.07420 | 0.7284524 |
| 13 | 42798837 | Not In Discovery | MX1 | -0.22 | 0.07640 | 0.7284524 |
| 169 | 1178192 | Not In Discovery | FAM132A | -0.22 | 0.07950 | 0.7284524 |
| 100 | 92414770 | Not In Discovery | BRDT | -0.22 | 0.08620 | 0.7284524 |
| 81 | 313408 | Not In Discovery | IFITM1 | -0.22 | 0.08640 | 0.7284524 |
| 197 | 33048581 | Not In Discovery | HLA-DPB1 | -0.23 | 0.08870 | 0.7284524 |
| 15 | 42798857 | Not In Discovery | MX1 | -0.21 | 0.08920 | 0.7284524 |
| 102 | 92414793 | Not In Discovery | BRDT | -0.21 | 0.09260 | 0.7284524 |
| 183 | 33048444 | Not In Discovery | HLA-DPB1 | -0.22 | 0.09630 | 0.7284524 |
| 187 | 33048502 | cg26645432 | HLA-DPB1 | -0.22 | 0.09770 | 0.7284524 |
| 99 | 92414751 | Not In Discovery | BRDT | -0.21 | 0.09860 | 0.7284524 |
| 8 | 42798781 | Not In Discovery | MX1 | -0.21 | 0.10100 | 0.7284524 |
| 101 | 92414782 | cg02935097 | BRDT | -0.20 | 0.10900 | 0.7284524 |
| 47 | 76145689 | Not In Discovery | UPK3B | 0.20 | 0.11200 | 0.7284524 |
| 4 | 42798733 | Not In Discovery | MX1 | -0.20 | 0.11300 | 0.7284524 |
| 80 | 313354 | cg11694510 | IFITM1 | -0.20 | 0.12100 | 0.7284524 |
| 195 | 33048571 | Not In Discovery | HLA-DPB1 | -0.20 | 0.12300 | 0.7284524 |
| 189 | 33048540 | cg14870156 | HLA-DPB1 | -0.20 | 0.12500 | 0.7284524 |
| 46 | 76145693 | Not In Discovery | UPK3B | 0.19 | 0.12600 | 0.7284524 |
| 193 | 33048555 | cg19990651 | HLA-DPB1 | -0.20 | 0.13000 | 0.7284524 |
| 98 | 92414737 | cg13299824 | BRDT | -0.19 | 0.13500 | 0.7284524 |
| 12 | 42798829 | Not In Discovery | MX1 | -0.19 | 0.13700 | 0.7284524 |
| 48 | 76145673 | cg05372444 | UPK3B | 0.19 | 0.14000 | 0.7284524 |
| 170 | 1178182 | Not In Discovery | FAM132A | -0.19 | 0.14000 | 0.7284524 |
| 180 | 33048417 | Not In Discovery | HLA-DPB1 | -0.19 | 0.14300 | 0.7284524 |
| 95 | 92414661 | Not In Discovery | BRDT | -0.19 | 0.14400 | 0.7284524 |
| 14 | 42798847 | Not In Discovery | MX1 | -0.18 | 0.14500 | 0.7284524 |
| 106 | 62199181 | cg06064964 | HELZ2 | 0.19 | 0.15200 | 0.7289091 |
| 171 | 1178172 | Not In Discovery | FAM132A | -0.18 | 0.15200 | 0.7289091 |
| 188 | 33048529 | cg06437840 | HLA-DPB1 | -0.18 | 0.16800 | 0.7843696 |
| 168 | 1178202 | Not In Discovery | FAM132A | -0.17 | 0.17100 | 0.7843696 |
| 10 | 42798816 | Not In Discovery | MX1 | -0.17 | 0.18400 | 0.8132292 |
| 9 | 42798813 | Not In Discovery | MX1 | -0.17 | 0.18500 | 0.8132292 |
| 20 | 30039132 | Not In Discovery | RNF39 | 0.17 | 0.19600 | 0.8382973 |
| 19 | 30039130 | Not In Discovery | RNF39 | 0.16 | 0.20500 | 0.8382973 |
| 182 | 33048433 | Not In Discovery | HLA-DPB1 | -0.17 | 0.21100 | 0.8382973 |
| 52 | 76145606 | Not In Discovery | UPK3B | 0.15 | 0.22600 | 0.8382973 |
| 94 | 92414650 | Not In Discovery | BRDT | -0.15 | 0.22700 | 0.8382973 |
| 97 | 92414722 | cg14732540 | BRDT | -0.15 | 0.23000 | 0.8382973 |
| 11 | 42798818 | Not In Discovery | MX1 | -0.15 | 0.23800 | 0.8382973 |
| 3 | 42798723 | Not In Discovery | MX1 | -0.15 | 0.23900 | 0.8382973 |
| 199 | 33048602 | Not In Discovery | HLA-DPB1 | -0.16 | 0.24000 | 0.8382973 |
| 96 | 92414719 | Not In Discovery | BRDT | -0.15 | 0.24500 | 0.8382973 |
| 124 | 37383730 | Not In Discovery | EIF2AK2 | -0.14 | 0.27800 | 0.8382973 |
| 5 | 42798747 | cg08924203 | MX1 | -0.14 | 0.28000 | 0.8382973 |
| 32 | 33048286 | cg09234582 | HLA-DPB1 | -0.14 | 0.28300 | 0.8382973 |
| 181 | 33048423 | Not In Discovery | HLA-DPB1 | -0.14 | 0.29000 | 0.8382973 |
| 107 | 62199190 | cg09844573 | HELZ2 | 0.14 | 0.29100 | 0.8382973 |
| 202 | 79085713 | cg17980508 | IFI44L | -0.14 | 0.29600 | 0.8382973 |
| 25 | 30039186 | Not In Discovery | RNF39 | 0.13 | 0.29700 | 0.8382973 |
| 22 | 30039151 | cg18930910 | RNF39 | 0.13 | 0.30300 | 0.8382973 |
| 71 | 30039418 | Not In Discovery | RNF39 | -0.12 | 0.33100 | 0.8382973 |
| 203 | 79085765 | cg00855901 | IFI44L | -0.13 | 0.33500 | 0.8382973 |
| 18 | 30039127 | Not In Discovery | RNF39 | 0.12 | 0.33900 | 0.8382973 |
| 33 | 33048291 | cg25045942 | HLA-DPB1 | -0.12 | 0.34000 | 0.8382973 |
| 89 | 12877276 | Not In Discovery | HOOK2 | -0.12 | 0.34300 | 0.8382973 |
| 24 | 30039175 | cg03343571 | RNF39 | 0.12 | 0.34600 | 0.8382973 |
| 184 | 33048469 | cg10850215 | HLA-DPB1 | -0.12 | 0.35200 | 0.8382973 |
| 34 | 33048310 | cg13349035 | HLA-DPB1 | -0.12 | 0.36200 | 0.8382973 |
| 179 | 92418017 | Not In Discovery | BRDT | -0.11 | 0.37000 | 0.8382973 |
| 104 | 62199061 | Not In Discovery | HELZ2 | 0.12 | 0.38000 | 0.8382973 |
| 40 | 75953935 | cg19367436 | COX7A2 | 0.11 | 0.38800 | 0.8382973 |
| 200 | 79085586 | cg03607951 | IFI44L | -0.11 | 0.38900 | 0.8382973 |
| 51 | 76145620 | Not In Discovery | UPK3B | 0.11 | 0.39700 | 0.8382973 |
| 76 | 30039476 | cg10930308 | RNF39 | -0.11 | 0.40500 | 0.8382973 |
| 83 | 12877107 | Not In Discovery | HOOK2 | -0.10 | 0.41400 | 0.8382973 |
| 21 | 30039142 | cg00947782 | RNF39 | 0.10 | 0.41700 | 0.8382973 |
| 82 | 12877099 | Not In Discovery | HOOK2 | -0.10 | 0.42000 | 0.8382973 |
| 140 | 12876911 | Not In Discovery | HOOK2 | -0.10 | 0.42800 | 0.8382973 |
| 139 | 12876918 | Not In Discovery | HOOK2 | -0.10 | 0.43000 | 0.8382973 |
| 53 | 76145589 | Not In Discovery | UPK3B | -0.10 | 0.43300 | 0.8382973 |
| 121 | 37383623 | Not In Discovery | EIF2AK2 | -0.10 | 0.43400 | 0.8382973 |
| 136 | 12876942 | Not In Discovery | HOOK2 | -0.10 | 0.43800 | 0.8382973 |
| 23 | 30039158 | Not In Discovery | RNF39 | 0.10 | 0.43900 | 0.8382973 |
| 135 | 12876944 | Not In Discovery | HOOK2 | -0.10 | 0.44100 | 0.8382973 |
| 154 | 179740906 | Not In Discovery | GFPT2 | 0.10 | 0.44100 | 0.8382973 |
| 17 | 30039123 | Not In Discovery | RNF39 | 0.10 | 0.44200 | 0.8382973 |
| 208 | 67361773 | cg24961286 | SMAD3 | 0.10 | 0.44300 | 0.8382973 |
| 36 | 75953821 | Not In Discovery | COX7A2 | 0.10 | 0.44900 | 0.8382973 |
| 132 | 12876969 | Not In Discovery | HOOK2 | -0.10 | 0.44900 | 0.8382973 |
| 138 | 12876926 | Not In Discovery | HOOK2 | -0.10 | 0.44900 | 0.8382973 |
| 151 | 179740920 | Not In Discovery | GFPT2 | 0.10 | 0.44900 | 0.8382973 |
| 134 | 12876946 | Not In Discovery | HOOK2 | -0.10 | 0.45100 | 0.8382973 |
| 131 | 12876987 | Not In Discovery | HOOK2 | -0.09 | 0.45500 | 0.8382973 |
| 84 | 12877138 | Not In Discovery | HOOK2 | -0.09 | 0.45700 | 0.8382973 |
| 128 | 12877001 | cg11738485 | HOOK2 | -0.09 | 0.45900 | 0.8382973 |
| 133 | 12876948 | Not In Discovery | HOOK2 | -0.09 | 0.46300 | 0.8382973 |
| 137 | 12876937 | Not In Discovery | HOOK2 | -0.09 | 0.46300 | 0.8382973 |
| 87 | 12877215 | Not In Discovery | HOOK2 | -0.09 | 0.46600 | 0.8382973 |
| 88 | 12877235 | Not In Discovery | HOOK2 | -0.09 | 0.46600 | 0.8382973 |
| 29 | 30039232 | Not In Discovery | RNF39 | 0.09 | 0.47000 | 0.8382973 |
| 129 | 12876997 | Not In Discovery | HOOK2 | -0.09 | 0.47200 | 0.8382973 |
| 130 | 12876993 | Not In Discovery | HOOK2 | -0.09 | 0.47500 | 0.8382973 |
| 156 | 179740888 | Not In Discovery | GFPT2 | 0.09 | 0.47600 | 0.8382973 |
| 55 | 30039274 | Not In Discovery | RNF39 | -0.09 | 0.47800 | 0.8382973 |
| 30 | 30039235 | Not In Discovery | RNF39 | 0.09 | 0.48100 | 0.8382973 |
| 146 | 179740963 | Not In Discovery | GFPT2 | 0.09 | 0.48400 | 0.8382973 |
| 209 | 67361798 | Not In Discovery | SMAD3 | 0.09 | 0.48800 | 0.8382973 |
| 112 | 179741101 | Not In Discovery | GFPT2 | 0.09 | 0.49000 | 0.8382973 |
| 147 | 179740957 | Not In Discovery | GFPT2 | 0.09 | 0.49000 | 0.8382973 |
| 145 | 179740970 | Not In Discovery | GFPT2 | 0.09 | 0.49400 | 0.8382973 |
| 127 | 12877020 | Not In Discovery | HOOK2 | -0.09 | 0.49900 | 0.8382973 |
| 148 | 179740955 | Not In Discovery | GFPT2 | 0.09 | 0.50400 | 0.8382973 |
| 31 | 30039239 | Not In Discovery | RNF39 | 0.09 | 0.50500 | 0.8382973 |
| 142 | 179740999 | Not In Discovery | GFPT2 | 0.08 | 0.50900 | 0.8382973 |
| 167 | 1178207 | Not In Discovery | FAM132A | -0.08 | 0.51000 | 0.8382973 |
| 141 | 179741008 | Not In Discovery | GFPT2 | 0.08 | 0.52200 | 0.8382973 |
| 155 | 179740900 | Not In Discovery | GFPT2 | 0.08 | 0.52300 | 0.8382973 |
| 67 | 30039403 | cg09279736 | RNF39 | -0.08 | 0.52600 | 0.8382973 |
| 152 | 179740918 | Not In Discovery | GFPT2 | 0.08 | 0.52600 | 0.8382973 |
| 143 | 179740994 | Not In Discovery | GFPT2 | 0.08 | 0.52900 | 0.8382973 |
| 57 | 30039303 | Not In Discovery | RNF39 | -0.08 | 0.53500 | 0.8382973 |
| 153 | 179740915 | cg13944838 | GFPT2 | 0.08 | 0.53700 | 0.8382973 |
| 105 | 62199156 | cg11779113 | HELZ2 | 0.08 | 0.54700 | 0.8382973 |
| 150 | 179740935 | Not In Discovery | GFPT2 | 0.08 | 0.55200 | 0.8382973 |
| 149 | 179740940 | Not In Discovery | GFPT2 | 0.08 | 0.55400 | 0.8382973 |
| 114 | 179741067 | Not In Discovery | GFPT2 | 0.08 | 0.55500 | 0.8382973 |
| 120 | 37383588 | Not In Discovery | EIF2AK2 | -0.08 | 0.55500 | 0.8382973 |
| 144 | 179740992 | Not In Discovery | GFPT2 | 0.07 | 0.55600 | 0.8382973 |
| 162 | 179740840 | Not In Discovery | GFPT2 | 0.07 | 0.55800 | 0.8382973 |
| 86 | 12877201 | Not In Discovery | HOOK2 | -0.07 | 0.55900 | 0.8382973 |
| 26 | 30039202 | Not In Discovery | RNF39 | 0.07 | 0.56000 | 0.8382973 |
| 1 | 42798695 | Not In Discovery | MX1 | -0.07 | 0.56800 | 0.8382973 |
| 85 | 12877188 | cg23899408 | HOOK2 | -0.07 | 0.56800 | 0.8382973 |
| 66 | 30039380 | cg13918754 | RNF39 | -0.07 | 0.56900 | 0.8382973 |
| 158 | 179740867 | Not In Discovery | GFPT2 | 0.07 | 0.57000 | 0.8382973 |
| 49 | 76145633 | cg16453056 | UPK3B | 0.07 | 0.57300 | 0.8382973 |
| 157 | 179740869 | Not In Discovery | GFPT2 | 0.07 | 0.57300 | 0.8382973 |
| 186 | 33048485 | cg17588455 | HLA-DPB1 | -0.07 | 0.58000 | 0.8382973 |
| 110 | 179741121 | cg02891314 | GFPT2 | 0.07 | 0.58200 | 0.8382973 |
| 161 | 179740852 | Not In Discovery | GFPT2 | 0.07 | 0.58200 | 0.8382973 |
| 64 | 30039374 | cg20249327 | RNF39 | -0.07 | 0.58700 | 0.8382973 |
| 41 | 75953937 | Not In Discovery | COX7A2 | 0.07 | 0.58800 | 0.8382973 |
| 65 | 30039376 | cg15877520 | RNF39 | -0.07 | 0.59700 | 0.8403198 |
| 117 | 179741042 | Not In Discovery | GFPT2 | 0.07 | 0.59900 | 0.8403198 |
| 2 | 42798698 | Not In Discovery | MX1 | -0.07 | 0.60200 | 0.8403198 |
| 116 | 179741060 | Not In Discovery | GFPT2 | 0.07 | 0.61000 | 0.8403198 |
| 115 | 179741063 | Not In Discovery | GFPT2 | 0.06 | 0.61600 | 0.8403198 |
| 126 | 38805839 | Not In Discovery | TLR1 | -0.10 | 0.61700 | 0.8403198 |
| 185 | 33048483 | cg03229061 | HLA-DPB1 | -0.07 | 0.61800 | 0.8403198 |
| 7 | 42798765 | Not In Discovery | MX1 | -0.06 | 0.62600 | 0.8403198 |
| 113 | 179741081 | Not In Discovery | GFPT2 | 0.06 | 0.62600 | 0.8403198 |
| 164 | 179740825 | Not In Discovery | GFPT2 | 0.06 | 0.63600 | 0.8403198 |
| 172 | 1178162 | Not In Discovery | FAM132A | -0.06 | 0.63600 | 0.8403198 |
| 69 | 30039411 | Not In Discovery | RNF39 | -0.06 | 0.63900 | 0.8403198 |
| 28 | 30039208 | Not In Discovery | RNF39 | 0.06 | 0.64700 | 0.8403198 |
| 37 | 75953829 | Not In Discovery | COX7A2 | 0.06 | 0.65200 | 0.8403198 |
| 165 | 179740822 | Not In Discovery | GFPT2 | 0.06 | 0.65800 | 0.8403198 |
| 111 | 179741105 | cg23248424 | GFPT2 | 0.06 | 0.66400 | 0.8403198 |
| 50 | 76145628 | Not In Discovery | UPK3B | 0.05 | 0.66900 | 0.8403198 |
| 159 | 179740861 | Not In Discovery | GFPT2 | 0.05 | 0.67000 | 0.8403198 |
| 163 | 179740832 | Not In Discovery | GFPT2 | 0.05 | 0.67300 | 0.8403198 |
| 123 | 37383713 | Not In Discovery | EIF2AK2 | 0.05 | 0.67600 | 0.8403198 |
| 204 | 312419 | Not In Discovery | IFITM1 | -0.06 | 0.67700 | 0.8403198 |
| 91 | 75954053 | cg25716013 | COX7A2 | -0.05 | 0.68100 | 0.8403198 |
| 206 | 312463 | Not In Discovery | IFITM1 | -0.06 | 0.68400 | 0.8403198 |
| 38 | 75953853 | cg06809298 | COX7A2 | 0.05 | 0.68500 | 0.8403198 |
| 58 | 30039307 | Not In Discovery | RNF39 | -0.05 | 0.69000 | 0.8403829 |
| 160 | 179740855 | Not In Discovery | GFPT2 | 0.05 | 0.69600 | 0.8403829 |
| 178 | 92417998 | cg01081438 | BRDT | 0.05 | 0.69700 | 0.8403829 |
| 118 | 179741039 | Not In Discovery | GFPT2 | 0.05 | 0.70300 | 0.8404438 |
| 210 | 67361821 | Not In Discovery | SMAD3 | 0.05 | 0.70600 | 0.8404438 |
| 45 | 76145702 | Not In Discovery | UPK3B | -0.05 | 0.70900 | 0.8404438 |
| 59 | 30039313 | Not In Discovery | RNF39 | -0.05 | 0.71500 | 0.8428212 |
| 56 | 30039278 | Not In Discovery | RNF39 | -0.05 | 0.72400 | 0.8486889 |
| 54 | 30039271 | Not In Discovery | RNF39 | -0.04 | 0.73200 | 0.8509180 |
| 73 | 30039435 | cg12633154 | RNF39 | -0.04 | 0.73500 | 0.8509180 |
| 68 | 30039408 | cg07382347 | RNF39 | -0.04 | 0.73800 | 0.8509180 |
| 176 | 1178105 | Not In Discovery | FAM132A | -0.04 | 0.75500 | 0.8657880 |
| 207 | 312518 | cg05432003 | IFITM1 | 0.06 | 0.76600 | 0.8736541 |
| 62 | 30039354 | Not In Discovery | RNF39 | -0.04 | 0.78500 | 0.8855266 |
| 42 | 75953960 | Not In Discovery | COX7A2 | 0.04 | 0.78700 | 0.8855266 |
| 174 | 1178136 | Not In Discovery | FAM132A | 0.03 | 0.78900 | 0.8855266 |
| 35 | 33048370 | Not In Discovery | HLA-DPB1 | -0.03 | 0.80200 | 0.8953545 |
| 27 | 30039206 | Not In Discovery | RNF39 | 0.03 | 0.82000 | 0.9069686 |
| 60 | 30039323 | Not In Discovery | RNF39 | -0.03 | 0.82100 | 0.9069686 |
| 90 | 75954022 | Not In Discovery | COX7A2 | -0.03 | 0.82800 | 0.9099375 |
| 39 | 75953883 | Not In Discovery | COX7A2 | 0.03 | 0.83500 | 0.9128756 |
| 93 | 75954122 | Not In Discovery | COX7A2 | -0.02 | 0.84700 | 0.9212216 |
| 72 | 30039432 | cg13401893 | RNF39 | -0.02 | 0.85500 | 0.9251538 |
| 74 | 30039442 | cg10568066 | RNF39 | -0.02 | 0.87000 | 0.9313838 |
| 63 | 30039364 | Not In Discovery | RNF39 | 0.02 | 0.87200 | 0.9313838 |
| 177 | 1178086 | Not In Discovery | FAM132A | -0.02 | 0.87400 | 0.9313838 |
| 61 | 30039349 | Not In Discovery | RNF39 | -0.02 | 0.88600 | 0.9394271 |
| 190 | 33048542 | Not In Discovery | HLA-DPB1 | -0.02 | 0.89700 | 0.9406650 |
| 205 | 312434 | Not In Discovery | IFITM1 | -0.02 | 0.89900 | 0.9406650 |
| 44 | 76145717 | Not In Discovery | UPK3B | 0.02 | 0.90500 | 0.9406650 |
| 175 | 1178118 | Not In Discovery | FAM132A | -0.02 | 0.90500 | 0.9406650 |
| 125 | 38805732 | cg02016764 | TLR1 | 0.02 | 0.91200 | 0.9428098 |
| 92 | 75954118 | Not In Discovery | COX7A2 | -0.01 | 0.91600 | 0.9428098 |
| 201 | 79085647 | Not In Discovery | IFI44L | -0.01 | 0.94200 | 0.9648641 |
| 43 | 75953974 | Not In Discovery | COX7A2 | 0.01 | 0.95700 | 0.9754928 |
| 166 | 1178246 | cg24345856 | FAM132A | 0.00 | 0.96900 | 0.9829760 |
| 70 | 30039415 | Not In Discovery | RNF39 | 0.00 | 0.98000 | 0.9893780 |
| 75 | 30039466 | cg16078649 | RNF39 | 0.00 | 0.99400 | 0.9960000 |
| 122 | 37383679 | Not In Discovery | EIF2AK2 | 0.00 | 0.99600 | 0.9960000 |
5.8.2 Figure33:Correlation of serum type I IFN alpha level and gene methylation in CD8+ T cells
5.9 Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells
5.9.1 Table 34:Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells
| CpGs | CpGnames | Gene | Corr.beta | P.value | FDR | |
|---|---|---|---|---|---|---|
| 108 | 122281939 | cg08122652 | PARP9 | -0.46 | 0.000181 | 0.0381910 |
| 109 | 122281975 | cg00959259 | PARP9 | -0.44 | 0.000420 | 0.0443100 |
| 96 | 92414719 | Not In Discovery | BRDT | -0.40 | 0.001040 | 0.0731467 |
| 119 | 37383568 | cg17326313 | EIF2AK2 | -0.39 | 0.001700 | 0.0773667 |
| 77 | 21572657 | cg18719665 | TTC39C | 0.38 | 0.001960 | 0.0773667 |
| 98 | 92414737 | cg13299824 | BRDT | -0.38 | 0.002200 | 0.0773667 |
| 97 | 92414722 | cg14732540 | BRDT | -0.36 | 0.003710 | 0.1095693 |
| 78 | 21572635 | cg05401069 | TTC39C | 0.35 | 0.004630 | 0.1095693 |
| 94 | 92414650 | Not In Discovery | BRDT | -0.34 | 0.006390 | 0.1095693 |
| 79 | 21572623 | cg12639429 | TTC39C | 0.33 | 0.006400 | 0.1095693 |
| 99 | 92414751 | Not In Discovery | BRDT | -0.34 | 0.006790 | 0.1095693 |
| 100 | 92414770 | Not In Discovery | BRDT | -0.34 | 0.007060 | 0.1095693 |
| 101 | 92414782 | cg02935097 | BRDT | -0.34 | 0.007130 | 0.1095693 |
| 95 | 92414661 | Not In Discovery | BRDT | -0.34 | 0.007270 | 0.1095693 |
| 102 | 92414793 | Not In Discovery | BRDT | -0.33 | 0.008290 | 0.1166127 |
| 49 | 76145633 | cg16453056 | UPK3B | 0.31 | 0.012600 | 0.1661625 |
| 103 | 62199034 | cg17593958 | HELZ2 | 0.33 | 0.013900 | 0.1725235 |
| 170 | 1178182 | Not In Discovery | FAM132A | -0.27 | 0.033200 | 0.3891778 |
| 31 | 30039239 | Not In Discovery | RNF39 | 0.26 | 0.037200 | 0.4131158 |
| 22 | 30039151 | cg18930910 | RNF39 | 0.24 | 0.056600 | 0.5266208 |
| 24 | 30039175 | cg03343571 | RNF39 | 0.24 | 0.057500 | 0.5266208 |
| 30 | 30039235 | Not In Discovery | RNF39 | 0.24 | 0.058100 | 0.5266208 |
| 120 | 37383588 | Not In Discovery | EIF2AK2 | -0.24 | 0.059700 | 0.5266208 |
| 171 | 1178172 | Not In Discovery | FAM132A | -0.24 | 0.059900 | 0.5266208 |
| 63 | 30039364 | Not In Discovery | RNF39 | 0.22 | 0.089200 | 0.7493458 |
| 173 | 1178150 | Not In Discovery | FAM132A | -0.21 | 0.092900 | 0.7493458 |
| 29 | 30039232 | Not In Discovery | RNF39 | 0.21 | 0.103000 | 0.7493458 |
| 39 | 75953883 | Not In Discovery | COX7A2 | -0.21 | 0.104000 | 0.7493458 |
| 81 | 313408 | Not In Discovery | IFITM1 | -0.20 | 0.108000 | 0.7493458 |
| 51 | 76145620 | Not In Discovery | UPK3B | 0.20 | 0.116000 | 0.7493458 |
| 15 | 42798857 | Not In Discovery | MX1 | -0.20 | 0.120000 | 0.7493458 |
| 47 | 76145689 | Not In Discovery | UPK3B | 0.19 | 0.127000 | 0.7493458 |
| 178 | 92417998 | cg01081438 | BRDT | 0.19 | 0.128000 | 0.7493458 |
| 168 | 1178202 | Not In Discovery | FAM132A | -0.19 | 0.130000 | 0.7493458 |
| 26 | 30039202 | Not In Discovery | RNF39 | 0.19 | 0.133000 | 0.7493458 |
| 27 | 30039206 | Not In Discovery | RNF39 | 0.19 | 0.136000 | 0.7493458 |
| 16 | 42798863 | Not In Discovery | MX1 | -0.19 | 0.139000 | 0.7493458 |
| 204 | 312419 | Not In Discovery | IFITM1 | -0.23 | 0.142000 | 0.7493458 |
| 106 | 62199181 | cg06064964 | HELZ2 | 0.20 | 0.148000 | 0.7493458 |
| 23 | 30039158 | Not In Discovery | RNF39 | 0.18 | 0.151000 | 0.7493458 |
| 209 | 67361798 | Not In Discovery | SMAD3 | 0.19 | 0.160000 | 0.7493458 |
| 25 | 30039186 | Not In Discovery | RNF39 | 0.18 | 0.162000 | 0.7493458 |
| 38 | 75953853 | cg06809298 | COX7A2 | -0.18 | 0.166000 | 0.7493458 |
| 13 | 42798837 | Not In Discovery | MX1 | -0.17 | 0.169000 | 0.7493458 |
| 12 | 42798829 | Not In Discovery | MX1 | -0.17 | 0.171000 | 0.7493458 |
| 48 | 76145673 | cg05372444 | UPK3B | 0.17 | 0.174000 | 0.7493458 |
| 80 | 313354 | cg11694510 | IFITM1 | -0.17 | 0.174000 | 0.7493458 |
| 113 | 179741081 | Not In Discovery | GFPT2 | -0.17 | 0.193000 | 0.7493458 |
| 202 | 79085713 | cg17980508 | IFI44L | -0.17 | 0.205000 | 0.7493458 |
| 90 | 75954022 | Not In Discovery | COX7A2 | -0.16 | 0.210000 | 0.7493458 |
| 111 | 179741105 | cg23248424 | GFPT2 | -0.16 | 0.217000 | 0.7493458 |
| 152 | 179740918 | Not In Discovery | GFPT2 | -0.15 | 0.225000 | 0.7493458 |
| 21 | 30039142 | cg00947782 | RNF39 | 0.15 | 0.229000 | 0.7493458 |
| 34 | 33048310 | cg13349035 | HLA-DPB1 | -0.15 | 0.229000 | 0.7493458 |
| 116 | 179741060 | Not In Discovery | GFPT2 | -0.15 | 0.235000 | 0.7493458 |
| 5 | 42798747 | cg08924203 | MX1 | -0.15 | 0.239000 | 0.7493458 |
| 43 | 75953974 | Not In Discovery | COX7A2 | -0.15 | 0.240000 | 0.7493458 |
| 110 | 179741121 | cg02891314 | GFPT2 | -0.15 | 0.246000 | 0.7493458 |
| 166 | 1178246 | cg24345856 | FAM132A | 0.15 | 0.249000 | 0.7493458 |
| 37 | 75953829 | Not In Discovery | COX7A2 | -0.15 | 0.251000 | 0.7493458 |
| 117 | 179741042 | Not In Discovery | GFPT2 | -0.15 | 0.252000 | 0.7493458 |
| 114 | 179741067 | Not In Discovery | GFPT2 | -0.15 | 0.256000 | 0.7493458 |
| 124 | 37383730 | Not In Discovery | EIF2AK2 | -0.15 | 0.264000 | 0.7493458 |
| 118 | 179741039 | Not In Discovery | GFPT2 | -0.14 | 0.270000 | 0.7493458 |
| 141 | 179741008 | Not In Discovery | GFPT2 | -0.14 | 0.274000 | 0.7493458 |
| 112 | 179741101 | Not In Discovery | GFPT2 | -0.14 | 0.275000 | 0.7493458 |
| 104 | 62199061 | Not In Discovery | HELZ2 | 0.15 | 0.276000 | 0.7493458 |
| 149 | 179740940 | Not In Discovery | GFPT2 | -0.14 | 0.276000 | 0.7493458 |
| 18 | 30039127 | Not In Discovery | RNF39 | 0.14 | 0.282000 | 0.7493458 |
| 44 | 76145717 | Not In Discovery | UPK3B | 0.14 | 0.290000 | 0.7493458 |
| 165 | 179740822 | Not In Discovery | GFPT2 | -0.13 | 0.292000 | 0.7493458 |
| 7 | 42798765 | Not In Discovery | MX1 | -0.13 | 0.293000 | 0.7493458 |
| 121 | 37383623 | Not In Discovery | EIF2AK2 | -0.14 | 0.293000 | 0.7493458 |
| 145 | 179740970 | Not In Discovery | GFPT2 | -0.13 | 0.293000 | 0.7493458 |
| 151 | 179740920 | Not In Discovery | GFPT2 | -0.13 | 0.299000 | 0.7493458 |
| 153 | 179740915 | cg13944838 | GFPT2 | -0.13 | 0.299000 | 0.7493458 |
| 196 | 33048575 | Not In Discovery | HLA-DPB1 | -0.14 | 0.303000 | 0.7493458 |
| 91 | 75954053 | cg25716013 | COX7A2 | -0.13 | 0.304000 | 0.7493458 |
| 172 | 1178162 | Not In Discovery | FAM132A | -0.13 | 0.304000 | 0.7493458 |
| 155 | 179740900 | Not In Discovery | GFPT2 | -0.13 | 0.305000 | 0.7493458 |
| 146 | 179740963 | Not In Discovery | GFPT2 | -0.13 | 0.312000 | 0.7493458 |
| 14 | 42798847 | Not In Discovery | MX1 | -0.13 | 0.315000 | 0.7493458 |
| 8 | 42798781 | Not In Discovery | MX1 | -0.13 | 0.318000 | 0.7493458 |
| 148 | 179740955 | Not In Discovery | GFPT2 | -0.13 | 0.321000 | 0.7493458 |
| 35 | 33048370 | Not In Discovery | HLA-DPB1 | -0.13 | 0.325000 | 0.7493458 |
| 115 | 179741063 | Not In Discovery | GFPT2 | -0.13 | 0.325000 | 0.7493458 |
| 199 | 33048602 | Not In Discovery | HLA-DPB1 | -0.13 | 0.329000 | 0.7493458 |
| 150 | 179740935 | Not In Discovery | GFPT2 | -0.12 | 0.332000 | 0.7493458 |
| 105 | 62199156 | cg11779113 | HELZ2 | 0.13 | 0.333000 | 0.7493458 |
| 156 | 179740888 | Not In Discovery | GFPT2 | -0.12 | 0.333000 | 0.7493458 |
| 3 | 42798723 | Not In Discovery | MX1 | -0.12 | 0.336000 | 0.7493458 |
| 143 | 179740994 | Not In Discovery | GFPT2 | -0.12 | 0.339000 | 0.7493458 |
| 144 | 179740992 | Not In Discovery | GFPT2 | -0.12 | 0.346000 | 0.7493458 |
| 50 | 76145628 | Not In Discovery | UPK3B | 0.12 | 0.348000 | 0.7493458 |
| 92 | 75954118 | Not In Discovery | COX7A2 | -0.12 | 0.348000 | 0.7493458 |
| 122 | 37383679 | Not In Discovery | EIF2AK2 | -0.12 | 0.349000 | 0.7493458 |
| 46 | 76145693 | Not In Discovery | UPK3B | 0.12 | 0.352000 | 0.7493458 |
| 147 | 179740957 | Not In Discovery | GFPT2 | -0.12 | 0.357000 | 0.7493458 |
| 93 | 75954122 | Not In Discovery | COX7A2 | -0.12 | 0.361000 | 0.7493458 |
| 10 | 42798816 | Not In Discovery | MX1 | -0.12 | 0.362000 | 0.7493458 |
| 142 | 179740999 | Not In Discovery | GFPT2 | -0.12 | 0.365000 | 0.7493458 |
| 89 | 12877276 | Not In Discovery | HOOK2 | -0.11 | 0.366000 | 0.7493458 |
| 28 | 30039208 | Not In Discovery | RNF39 | 0.12 | 0.367000 | 0.7493458 |
| 76 | 30039476 | cg10930308 | RNF39 | -0.11 | 0.375000 | 0.7493458 |
| 154 | 179740906 | Not In Discovery | GFPT2 | -0.11 | 0.378000 | 0.7493458 |
| 6 | 42798749 | Not In Discovery | MX1 | -0.11 | 0.380000 | 0.7493458 |
| 203 | 79085765 | cg00855901 | IFI44L | -0.12 | 0.380000 | 0.7493458 |
| 163 | 179740832 | Not In Discovery | GFPT2 | -0.11 | 0.399000 | 0.7781835 |
| 159 | 179740861 | Not In Discovery | GFPT2 | -0.11 | 0.402000 | 0.7781835 |
| 9 | 42798813 | Not In Discovery | MX1 | -0.10 | 0.414000 | 0.7941273 |
| 11 | 42798818 | Not In Discovery | MX1 | -0.10 | 0.430000 | 0.8029204 |
| 157 | 179740869 | Not In Discovery | GFPT2 | -0.10 | 0.430000 | 0.8029204 |
| 158 | 179740867 | Not In Discovery | GFPT2 | -0.10 | 0.430000 | 0.8029204 |
| 162 | 179740840 | Not In Discovery | GFPT2 | -0.10 | 0.442000 | 0.8138571 |
| 189 | 33048540 | cg14870156 | HLA-DPB1 | -0.10 | 0.447000 | 0.8138571 |
| 58 | 30039307 | Not In Discovery | RNF39 | -0.10 | 0.456000 | 0.8138571 |
| 164 | 179740825 | Not In Discovery | GFPT2 | -0.09 | 0.460000 | 0.8138571 |
| 160 | 179740855 | Not In Discovery | GFPT2 | -0.09 | 0.491000 | 0.8138571 |
| 167 | 1178207 | Not In Discovery | FAM132A | -0.09 | 0.496000 | 0.8138571 |
| 88 | 12877235 | Not In Discovery | HOOK2 | -0.09 | 0.497000 | 0.8138571 |
| 36 | 75953821 | Not In Discovery | COX7A2 | -0.09 | 0.498000 | 0.8138571 |
| 32 | 33048286 | cg09234582 | HLA-DPB1 | -0.09 | 0.501000 | 0.8138571 |
| 161 | 179740852 | Not In Discovery | GFPT2 | -0.09 | 0.501000 | 0.8138571 |
| 190 | 33048542 | Not In Discovery | HLA-DPB1 | 0.09 | 0.509000 | 0.8138571 |
| 200 | 79085586 | cg03607951 | IFI44L | -0.09 | 0.515000 | 0.8138571 |
| 125 | 38805732 | cg02016764 | TLR1 | 0.12 | 0.521000 | 0.8138571 |
| 208 | 67361773 | cg24961286 | SMAD3 | 0.09 | 0.523000 | 0.8138571 |
| 54 | 30039271 | Not In Discovery | RNF39 | -0.08 | 0.524000 | 0.8138571 |
| 198 | 33048592 | Not In Discovery | HLA-DPB1 | -0.09 | 0.525000 | 0.8138571 |
| 52 | 76145606 | Not In Discovery | UPK3B | -0.08 | 0.533000 | 0.8138571 |
| 42 | 75953960 | Not In Discovery | COX7A2 | -0.08 | 0.538000 | 0.8138571 |
| 65 | 30039376 | cg15877520 | RNF39 | -0.07 | 0.560000 | 0.8138571 |
| 192 | 33048549 | Not In Discovery | HLA-DPB1 | -0.08 | 0.562000 | 0.8138571 |
| 210 | 67361821 | Not In Discovery | SMAD3 | 0.08 | 0.567000 | 0.8138571 |
| 33 | 33048291 | cg25045942 | HLA-DPB1 | -0.07 | 0.571000 | 0.8138571 |
| 177 | 1178086 | Not In Discovery | FAM132A | -0.07 | 0.579000 | 0.8138571 |
| 75 | 30039466 | cg16078649 | RNF39 | -0.07 | 0.580000 | 0.8138571 |
| 59 | 30039313 | Not In Discovery | RNF39 | -0.07 | 0.584000 | 0.8138571 |
| 62 | 30039354 | Not In Discovery | RNF39 | -0.07 | 0.586000 | 0.8138571 |
| 123 | 37383713 | Not In Discovery | EIF2AK2 | -0.07 | 0.587000 | 0.8138571 |
| 185 | 33048483 | cg03229061 | HLA-DPB1 | -0.07 | 0.587000 | 0.8138571 |
| 136 | 12876942 | Not In Discovery | HOOK2 | -0.07 | 0.588000 | 0.8138571 |
| 64 | 30039374 | cg20249327 | RNF39 | -0.07 | 0.594000 | 0.8138571 |
| 181 | 33048423 | Not In Discovery | HLA-DPB1 | -0.07 | 0.595000 | 0.8138571 |
| 131 | 12876987 | Not In Discovery | HOOK2 | -0.07 | 0.597000 | 0.8138571 |
| 140 | 12876911 | Not In Discovery | HOOK2 | -0.07 | 0.598000 | 0.8138571 |
| 129 | 12876997 | Not In Discovery | HOOK2 | -0.07 | 0.599000 | 0.8138571 |
| 74 | 30039442 | cg10568066 | RNF39 | 0.07 | 0.600000 | 0.8138571 |
| 87 | 12877215 | Not In Discovery | HOOK2 | -0.07 | 0.600000 | 0.8138571 |
| 82 | 12877099 | Not In Discovery | HOOK2 | -0.07 | 0.601000 | 0.8138571 |
| 132 | 12876969 | Not In Discovery | HOOK2 | -0.07 | 0.601000 | 0.8138571 |
| 138 | 12876926 | Not In Discovery | HOOK2 | -0.07 | 0.601000 | 0.8138571 |
| 135 | 12876944 | Not In Discovery | HOOK2 | -0.07 | 0.602000 | 0.8138571 |
| 83 | 12877107 | Not In Discovery | HOOK2 | -0.07 | 0.603000 | 0.8138571 |
| 206 | 312463 | Not In Discovery | IFITM1 | -0.08 | 0.606000 | 0.8138571 |
| 128 | 12877001 | cg11738485 | HOOK2 | -0.06 | 0.610000 | 0.8138571 |
| 134 | 12876946 | Not In Discovery | HOOK2 | -0.06 | 0.612000 | 0.8138571 |
| 130 | 12876993 | Not In Discovery | HOOK2 | -0.06 | 0.614000 | 0.8138571 |
| 137 | 12876937 | Not In Discovery | HOOK2 | -0.06 | 0.614000 | 0.8138571 |
| 133 | 12876948 | Not In Discovery | HOOK2 | -0.06 | 0.618000 | 0.8138571 |
| 139 | 12876918 | Not In Discovery | HOOK2 | -0.06 | 0.621000 | 0.8138571 |
| 19 | 30039130 | Not In Discovery | RNF39 | 0.06 | 0.626000 | 0.8153457 |
| 127 | 12877020 | Not In Discovery | HOOK2 | -0.06 | 0.631000 | 0.8160361 |
| 40 | 75953935 | cg19367436 | COX7A2 | -0.06 | 0.639000 | 0.8160361 |
| 66 | 30039380 | cg13918754 | RNF39 | -0.06 | 0.641000 | 0.8160361 |
| 86 | 12877201 | Not In Discovery | HOOK2 | -0.06 | 0.642000 | 0.8160361 |
| 53 | 76145589 | Not In Discovery | UPK3B | 0.06 | 0.648000 | 0.8176250 |
| 4 | 42798733 | Not In Discovery | MX1 | -0.06 | 0.651000 | 0.8176250 |
| 20 | 30039132 | Not In Discovery | RNF39 | 0.06 | 0.660000 | 0.8183873 |
| 84 | 12877138 | Not In Discovery | HOOK2 | -0.06 | 0.663000 | 0.8183873 |
| 17 | 30039123 | Not In Discovery | RNF39 | 0.06 | 0.667000 | 0.8183873 |
| 175 | 1178118 | Not In Discovery | FAM132A | 0.05 | 0.669000 | 0.8183873 |
| 1 | 42798695 | Not In Discovery | MX1 | 0.05 | 0.671000 | 0.8183873 |
| 183 | 33048444 | Not In Discovery | HLA-DPB1 | -0.05 | 0.686000 | 0.8318736 |
| 194 | 33048558 | cg01132696 | HLA-DPB1 | -0.05 | 0.695000 | 0.8368068 |
| 207 | 312518 | cg05432003 | IFITM1 | 0.08 | 0.698000 | 0.8368068 |
| 41 | 75953937 | Not In Discovery | COX7A2 | -0.05 | 0.709000 | 0.8451921 |
| 193 | 33048555 | cg19990651 | HLA-DPB1 | -0.05 | 0.718000 | 0.8511124 |
| 57 | 30039303 | Not In Discovery | RNF39 | -0.05 | 0.726000 | 0.8522056 |
| 70 | 30039415 | Not In Discovery | RNF39 | -0.04 | 0.727000 | 0.8522056 |
| 107 | 62199190 | cg09844573 | HELZ2 | 0.04 | 0.745000 | 0.8654385 |
| 182 | 33048433 | Not In Discovery | HLA-DPB1 | -0.04 | 0.753000 | 0.8654385 |
| 60 | 30039323 | Not In Discovery | RNF39 | -0.04 | 0.754000 | 0.8654385 |
| 174 | 1178136 | Not In Discovery | FAM132A | -0.04 | 0.764000 | 0.8654385 |
| 211 | 67361896 | Not In Discovery | SMAD3 | 0.04 | 0.765000 | 0.8654385 |
| 71 | 30039418 | Not In Discovery | RNF39 | -0.04 | 0.766000 | 0.8654385 |
| 85 | 12877188 | cg23899408 | HOOK2 | -0.04 | 0.767000 | 0.8654385 |
| 72 | 30039432 | cg13401893 | RNF39 | 0.04 | 0.774000 | 0.8686915 |
| 69 | 30039411 | Not In Discovery | RNF39 | -0.03 | 0.803000 | 0.8964709 |
| 126 | 38805839 | Not In Discovery | TLR1 | 0.04 | 0.822000 | 0.9067590 |
| 56 | 30039278 | Not In Discovery | RNF39 | -0.03 | 0.832000 | 0.9067590 |
| 55 | 30039274 | Not In Discovery | RNF39 | -0.03 | 0.833000 | 0.9067590 |
| 186 | 33048485 | cg17588455 | HLA-DPB1 | -0.03 | 0.836000 | 0.9067590 |
| 188 | 33048529 | cg06437840 | HLA-DPB1 | -0.03 | 0.838000 | 0.9067590 |
| 197 | 33048581 | Not In Discovery | HLA-DPB1 | -0.03 | 0.838000 | 0.9067590 |
| 180 | 33048417 | Not In Discovery | HLA-DPB1 | 0.02 | 0.853000 | 0.9136193 |
| 205 | 312434 | Not In Discovery | IFITM1 | 0.03 | 0.853000 | 0.9136193 |
| 176 | 1178105 | Not In Discovery | FAM132A | -0.02 | 0.860000 | 0.9150402 |
| 195 | 33048571 | Not In Discovery | HLA-DPB1 | -0.02 | 0.863000 | 0.9150402 |
| 2 | 42798698 | Not In Discovery | MX1 | -0.02 | 0.876000 | 0.9202525 |
| 179 | 92418017 | Not In Discovery | BRDT | -0.02 | 0.878000 | 0.9202525 |
| 184 | 33048469 | cg10850215 | HLA-DPB1 | 0.02 | 0.881000 | 0.9202525 |
| 73 | 30039435 | cg12633154 | RNF39 | -0.02 | 0.902000 | 0.9375468 |
| 68 | 30039408 | cg07382347 | RNF39 | -0.01 | 0.909000 | 0.9401912 |
| 187 | 33048502 | cg26645432 | HLA-DPB1 | -0.01 | 0.918000 | 0.9448683 |
| 169 | 1178192 | Not In Discovery | FAM132A | -0.01 | 0.926000 | 0.9484757 |
| 45 | 76145702 | Not In Discovery | UPK3B | -0.01 | 0.939000 | 0.9571449 |
| 201 | 79085647 | Not In Discovery | IFI44L | -0.01 | 0.950000 | 0.9611100 |
| 67 | 30039403 | cg09279736 | RNF39 | -0.01 | 0.952000 | 0.9611100 |
| 61 | 30039349 | Not In Discovery | RNF39 | -0.01 | 0.968000 | 0.9726095 |
| 191 | 33048544 | Not In Discovery | HLA-DPB1 | 0.00 | 0.973000 | 0.9730000 |
5.9.2 Figure34:Correlation of serum type I IFN beta level and gene methylation in CD8+ T cells
5.10 PartIV Summary:
In this part, we explored the differential serum content of type I IFN alpha and IFN beta between SSc patients and Controls. According to our dataset, we found significantly higher serum type I IFN alpha as well as beta levels in SSc patients, indicating its abnormalty in SSc pathogenesis, and it was concordant with previous datasets as well as the datasets in SLE patients. In addition to the differential content of serum type I IFN, we also explored its correlation with gene expression and methylation. In general, we found that, the IFN related genes showed increased gene expression as the increase of type I IFN alpha/beta, and showed decreased gene methylation as the increase of type I IFN alpha/beta. This results was concordant with the previous Part III result that suggested the negative correlation between gene expression and methylation in IFN related genes.
6 Part V: INF treating for Cell Line
6.1 The Jurket Cell Analysis
| Gene | POS | Avg.Base | Normal | IFN.a.6 | IFN.b.6 | IFN.ab.6 | IFN.a.12 | IFN.b.12 | IFN.ab.12 | Min.Fold | Max.Fold | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 239 | IFITM1_ | 312518 | 49.56863 | 0.1808279 | 0.2186960 | 0.1362536 | 0.1658155 | 0.1542028 | 0.1497752 | 0.1617978 | 0.7534987 | 1.2094153 |
| 226 | HLA-DPB1_ | 33048542 | 6509.50943 | 0.0036763 | 0.0037293 | 0.0032093 | 0.0028211 | 0.0039949 | 0.0043449 | 0.0039498 | 0.7673814 | 1.1818781 |
| 151 | EIF2AK2_ | 37383730 | 8206.24528 | 0.0171492 | 0.0163116 | 0.0152293 | 0.0133239 | 0.0168189 | 0.0140194 | 0.0162482 | 0.7769373 | 0.9807383 |
| 149 | EIF2AK2_ | 37383679 | 8206.28302 | 0.0185175 | 0.0173858 | 0.0161690 | 0.0171169 | 0.0149471 | 0.0165643 | 0.0169265 | 0.8071895 | 0.9388868 |
| 148 | EIF2AK2_ | 37383623 | 8218.43396 | 0.0144687 | 0.0136239 | 0.0132008 | 0.0120720 | 0.0116902 | 0.0141835 | 0.0151972 | 0.8079680 | 1.0503529 |
| 241 | IFI44L_ | 79085647 | 27.94340 | 0.2645299 | 0.3018890 | 0.4836957 | 0.2175325 | 0.3421325 | 0.3544292 | 0.3333333 | 0.8223360 | 1.8285102 |
| 214 | BRDT_2 | 92417998 | 2442.32075 | 0.0385421 | 0.0394334 | 0.0433417 | 0.0633226 | 0.0330661 | 0.0361959 | 0.0358999 | 0.8579229 | 1.6429488 |
| 202 | FAM132A_ | 1178246 | 2862.20755 | 0.0735571 | 0.0638543 | 0.0727095 | 0.0688066 | 0.0721988 | 0.0841401 | 0.0785009 | 0.8680915 | 1.1438747 |
| 132 | HELZ2_ | 62199190 | 2844.45283 | 0.0110791 | 0.0104221 | 0.0097193 | 0.0096732 | 0.0128305 | 0.0127949 | 0.0139698 | 0.8731008 | 1.2609178 |
| 146 | EIF2AK2_ | 37383568 | 8208.30189 | 0.1806969 | 0.1597281 | 0.1628359 | 0.1635589 | 0.1631069 | 0.1639120 | 0.1688722 | 0.8839558 | 0.9345605 |
| 38 | CCDC85C_ | 100069693 | 125.61538 | 0.9474747 | 0.9307531 | 0.9114478 | 0.8447430 | 0.9025301 | 0.9098232 | 0.9105894 | 0.8915731 | 0.9823513 |
| 24 | CCDC85C_ | 100069585 | 125.71154 | 0.9398990 | 0.8978261 | 0.8382353 | 0.8613908 | 0.8783589 | 0.8812267 | 0.8916911 | 0.8918355 | 0.9552368 |
| 168 | HOOK2_2 | 12876969 | 41338.60377 | 0.0311405 | 0.0296678 | 0.0307192 | 0.0328163 | 0.0278030 | 0.0282222 | 0.0285883 | 0.8928228 | 1.0538123 |
| 167 | HOOK2_2 | 12876987 | 41339.35849 | 0.0279196 | 0.0270365 | 0.0279717 | 0.0308079 | 0.0252206 | 0.0264513 | 0.0249635 | 0.8941228 | 1.1034512 |
| 169 | HOOK2_2 | 12876948 | 41352.96226 | 0.0348022 | 0.0343632 | 0.0351502 | 0.0372277 | 0.0324302 | 0.0314338 | 0.0325705 | 0.9032122 | 1.0696926 |
| 147 | EIF2AK2_ | 37383588 | 8208.79245 | 0.0662880 | 0.0673229 | 0.0668573 | 0.0699649 | 0.0752748 | 0.0598727 | 0.0687655 | 0.9032206 | 1.1355713 |
| 89 | UPK3B_2 | 76145589 | 5753.64151 | 0.3647373 | 0.3478331 | 0.3593414 | 0.3521429 | 0.3573062 | 0.3534394 | 0.3337164 | 0.9149500 | 0.9852061 |
| 166 | HOOK2_2 | 12876993 | 41338.73585 | 0.0275662 | 0.0268339 | 0.0284840 | 0.0302059 | 0.0257795 | 0.0252260 | 0.0276297 | 0.9151081 | 1.0957600 |
| 150 | EIF2AK2_ | 37383713 | 8206.37736 | 0.0116287 | 0.0136651 | 0.0107156 | 0.0106978 | 0.0143946 | 0.0123623 | 0.0114399 | 0.9199461 | 1.2378560 |
| 129 | HELZ2_ | 62199061 | 2844.77358 | 0.0132565 | 0.0153742 | 0.0122007 | 0.0152167 | 0.0161666 | 0.0211720 | 0.0152074 | 0.9203551 | 1.5970967 |
| 37 | CCDC85C_ | 100069687 | 125.61538 | 0.9813131 | 0.9519357 | 0.9463095 | 0.9035486 | 0.9448893 | 0.9473016 | 0.9278222 | 0.9207546 | 0.9700631 |
| 243 | IFI44L_ | 79085765 | 27.94340 | 0.9017705 | 0.9406107 | 0.8635223 | 0.9056412 | 0.8500690 | 0.8492134 | 0.8333333 | 0.9241080 | 1.0430711 |
| 32 | CCDC85C_ | 100069657 | 125.61538 | 0.9666667 | 0.9809297 | 0.9315745 | 0.9606593 | 0.9732967 | 0.9476061 | 0.8960040 | 0.9269007 | 1.0147549 |
| 165 | HOOK2_2 | 12876997 | 41340.37736 | 0.0227380 | 0.0225993 | 0.0228712 | 0.0256441 | 0.0211053 | 0.0212729 | 0.0223000 | 0.9281970 | 1.1278104 |
| 237 | IFITM1_ | 312434 | 68.35294 | 0.9571429 | 0.9606661 | 0.8905736 | 0.9644419 | 0.9437767 | 0.9630154 | 0.9498922 | 0.9304500 | 1.0076259 |
| 121 | HOOK2_ | 12877188 | 21370.73585 | 0.1143300 | 0.1066673 | 0.1141502 | 0.1131671 | 0.1096066 | 0.1130287 | 0.1156642 | 0.9329767 | 1.0116693 |
| 23 | CCDC85C_ | 100069566 | 125.69231 | 0.9717172 | 0.9497206 | 0.9435224 | 0.9520768 | 0.9075720 | 0.9463099 | 0.9359238 | 0.9339879 | 0.9797880 |
| 46 | CCDC85C_ | 100069724 | 125.61538 | 0.9328283 | 0.8811140 | 0.8903326 | 0.8878633 | 0.9311565 | 0.8842634 | 0.8713786 | 0.9341254 | 0.9982078 |
| 173 | HOOK2_2 | 12876937 | 41339.18868 | 0.0319246 | 0.0313413 | 0.0317690 | 0.0336976 | 0.0299407 | 0.0304477 | 0.0304109 | 0.9378577 | 1.0555361 |
| 238 | IFITM1_ | 312463 | 82.53846 | 0.7617845 | 0.7555911 | 0.7150287 | 0.7559719 | 0.7477820 | 0.7495064 | 0.7905397 | 0.9386233 | 1.0377472 |
6.2 The TH Cell Analysis
| Gene | POS | Avg.Base | Normal | IFN.a.6 | IFN.b.6 | IFN.ab.6 | IFN.a.12 | IFN.b.12 | IFN.ab.12 | IFN.a.24 | IFN.b.24 | IFN.ab.24 | Min.Fold | Max.Fold | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 235 | HLA-DPB1_ | 33048602 | 6509.35849 | 0.0010416 | 0.0008355 | 0.0008486 | 0.0009521 | 0.0000760 | 0.0016394 | 0.0013623 | 0.0013274 | 0.0010804 | 0.0011045 | 0.0729386 | 1.5738292 |
| 128 | HELZ2_ | 62199034 | 2844.77358 | 0.0163626 | 0.0120537 | 0.0125538 | 0.0126250 | 0.0178672 | 0.0163562 | 0.0142813 | 0.0099055 | 0.0130293 | 0.0231127 | 0.6053757 | 1.4125345 |
| 239 | IFITM1_ | 312518 | 49.56863 | 0.1490106 | 0.1620424 | 0.2938782 | 0.2429481 | 0.0937500 | 0.1952381 | 0.2379085 | 0.2704348 | 0.1905330 | 0.2757508 | 0.6291497 | 1.9721962 |
| 130 | HELZ2_ | 62199156 | 2844.43396 | 0.0149910 | 0.0126899 | 0.0096051 | 0.0132248 | 0.0144247 | 0.0119805 | 0.0119481 | 0.0115317 | 0.0102701 | 0.0102203 | 0.6407231 | 0.9622219 |
| 150 | EIF2AK2_ | 37383713 | 8206.37736 | 0.0147414 | 0.0134571 | 0.0160120 | 0.0124505 | 0.0136681 | 0.0162727 | 0.0121974 | 0.0097826 | 0.0132909 | 0.0130054 | 0.6636154 | 1.1038736 |
| 148 | EIF2AK2_ | 37383623 | 8218.43396 | 0.0099360 | 0.0073559 | 0.0100664 | 0.0069197 | 0.0147517 | 0.0114611 | 0.0102307 | 0.0074173 | 0.0091063 | 0.0085628 | 0.6964240 | 1.4846702 |
| 241 | IFI44L_ | 79085647 | 27.94340 | 0.4957265 | 0.4563889 | 0.3761905 | 0.5109215 | 0.4450275 | 0.4936636 | 0.5121672 | 0.5092593 | 0.3478931 | 0.4920635 | 0.7017843 | 1.0331648 |
| 132 | HELZ2_ | 62199190 | 2844.45283 | 0.0058042 | 0.0061712 | 0.0043537 | 0.0082894 | 0.0066653 | 0.0049752 | 0.0055615 | 0.0091815 | 0.0058678 | 0.0046162 | 0.7500990 | 1.5818638 |
| 226 | HLA-DPB1_ | 33048542 | 6509.50943 | 0.0036818 | 0.0042313 | 0.0031407 | 0.0040973 | 0.0028111 | 0.0041452 | 0.0045267 | 0.0041168 | 0.0037529 | 0.0042136 | 0.7635244 | 1.2294829 |
| 131 | HELZ2_ | 62199181 | 2844.35849 | 0.0100858 | 0.0101316 | 0.0120197 | 0.0092691 | 0.0132344 | 0.0087280 | 0.0141614 | 0.0079786 | 0.0127125 | 0.0095089 | 0.7910677 | 1.4040892 |
| 49 | SMAD3_ | 67361773 | 968.00000 | 0.0340764 | 0.0684762 | 0.0299690 | 0.0370159 | 0.2053004 | 0.0345706 | 0.0332370 | 0.0370977 | 0.0284410 | 0.0280352 | 0.8227175 | 6.0247161 |
| 146 | EIF2AK2_ | 37383568 | 8208.30189 | 0.0233245 | 0.0228477 | 0.0208581 | 0.0266197 | 0.0193369 | 0.0231148 | 0.0205561 | 0.0247085 | 0.0241278 | 0.0199855 | 0.8290384 | 1.1412748 |
| 89 | UPK3B_2 | 76145589 | 5753.64151 | 0.0723433 | 0.0737401 | 0.0669883 | 0.0742428 | 0.0602158 | 0.0747420 | 0.0767285 | 0.0701024 | 0.0805793 | 0.0778624 | 0.8323619 | 1.1138463 |
| 28 | CCDC85C_ | 100069619 | 125.88462 | 0.6422388 | 0.6427889 | 0.6304749 | 0.6358018 | 0.5948387 | 0.5456341 | 0.6416545 | 0.6532609 | 0.6545285 | 0.6332129 | 0.8495814 | 1.0191358 |
| 214 | BRDT_2 | 92417998 | 2442.32075 | 0.6421807 | 0.5854239 | 0.6359689 | 0.6341804 | 0.5497847 | 0.6355117 | 0.6460720 | 0.6466256 | 0.6425822 | 0.6483927 | 0.8561214 | 1.0096732 |
| 149 | EIF2AK2_ | 37383679 | 8206.28302 | 0.0188665 | 0.0214736 | 0.0232734 | 0.0221736 | 0.0253922 | 0.0224347 | 0.0214525 | 0.0210027 | 0.0162439 | 0.0214373 | 0.8609952 | 1.3458881 |
| 81 | UPK3B_2 | 76145702 | 5753.62264 | 0.0828763 | 0.0769159 | 0.0818970 | 0.0788093 | 0.0730590 | 0.0755363 | 0.0885223 | 0.0797858 | 0.0808496 | 0.0797531 | 0.8815426 | 1.0681260 |
| 54 | COX7A2_2 | 75953829 | 5082.01887 | 0.0344082 | 0.0387057 | 0.0373409 | 0.0323329 | 0.0306224 | 0.0366847 | 0.0385331 | 0.0384854 | 0.0339828 | 0.0390109 | 0.8899751 | 1.1337678 |
| 238 | IFITM1_ | 312463 | 82.53846 | 0.8557809 | 0.8126355 | 0.8547169 | 0.8645941 | 0.8173401 | 0.8581489 | 0.7791667 | 0.8078078 | 0.8193626 | 0.8890826 | 0.9104744 | 1.0389138 |
| 243 | IFI44L_ | 79085765 | 27.94340 | 0.8896215 | 0.9591667 | 0.9357143 | 0.8654528 | 0.8123438 | 0.8784562 | 0.9349980 | 0.9153439 | 0.8553545 | 0.9306157 | 0.9131342 | 1.0781739 |
| 52 | SMAD3_ | 67361896 | 968.18868 | 0.9666215 | 0.9464186 | 0.9608842 | 0.9649444 | 0.8878476 | 0.9651946 | 0.9653679 | 0.9677906 | 0.9677688 | 0.9577458 | 0.9185060 | 1.0012095 |
| 242 | IFI44L_ | 79085713 | 27.94340 | 0.9819292 | 1.0000000 | 0.9523810 | 0.9360279 | 0.9855072 | 0.9677419 | 0.9825721 | 0.9021164 | 0.9833333 | 0.9457672 | 0.9187184 | 1.0184034 |
| 59 | COX7A2_2 | 75953960 | 5081.92453 | 0.0783989 | 0.0813104 | 0.0803097 | 0.0752622 | 0.0720848 | 0.0774212 | 0.0859859 | 0.0840107 | 0.0777620 | 0.0839639 | 0.9194620 | 1.0967749 |
| 80 | UPK3B_2 | 76145717 | 5752.32075 | 0.2181485 | 0.2304175 | 0.2295617 | 0.2116299 | 0.2018941 | 0.2302342 | 0.2222051 | 0.2207743 | 0.2471065 | 0.2297214 | 0.9254892 | 1.1327445 |
| 46 | CCDC85C_ | 100069724 | 125.61538 | 0.9138886 | 0.8868305 | 0.9168022 | 0.8958383 | 0.8505376 | 0.8937438 | 0.8830009 | 0.9029503 | 0.9068599 | 0.8988424 | 0.9306798 | 1.0031882 |
| 147 | EIF2AK2_ | 37383588 | 8208.79245 | 0.0358746 | 0.0334038 | 0.0415256 | 0.0373750 | 0.0336848 | 0.0338408 | 0.0378366 | 0.0381385 | 0.0413846 | 0.0380144 | 0.9311264 | 1.1575208 |
| 176 | HOOK2_2 | 12876911 | 41093.18868 | 0.5373469 | 0.5025463 | 0.5548718 | 0.5384887 | 0.5493738 | 0.5457516 | 0.5586327 | 0.5581653 | 0.5548666 | 0.5538520 | 0.9352363 | 1.0396128 |
| 83 | UPK3B_2 | 76145689 | 5765.98113 | 0.2612200 | 0.2618450 | 0.2551548 | 0.2451893 | 0.2580878 | 0.2544979 | 0.2609420 | 0.2542030 | 0.2672785 | 0.2560899 | 0.9386311 | 1.0231930 |
| 104 | RNF39_ | 30039408 | 767.16981 | 0.7383827 | 0.7295692 | 0.7475960 | 0.7363309 | 0.6932901 | 0.7498446 | 0.7339636 | 0.7576127 | 0.7429396 | 0.7578557 | 0.9389306 | 1.0263726 |
| 162 | TLR1_ | 38805839 | 487.56604 | 0.5583725 | 0.5733711 | 0.5711377 | 0.5337995 | 0.5465214 | 0.5872620 | 0.5249235 | 0.5312232 | 0.5462176 | 0.5687931 | 0.9400955 | 1.0517387 |
7 Part VI: The Methylation Status of the Differentially Methylated CpGsites in other autoimmune diseases
7.1 SLE.CD4+ versus SSc.CD4+
| Gene | Cgsite | POS | McaM.SSc | McoM.SSc | Pvalue.SSc | FoldChange.SSc | McaM.SLE | McoM.SLE | Pvalue.SLE | FoldChange.SLE | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 317186 | EIF2AK2 | 37383568 | 37383568 | 0.1233814 | 0.1826725 | 0.0000315 | 0.6754238 | 0.1555306 | 0.3130137 | 0.0000000 | 0.4968810 |
| 20158 | PARP9 | 122281975 | 122281975 | 0.4276390 | 0.5290290 | 0.0000693 | 0.8083470 | 0.3579342 | 0.6517962 | 0.0000000 | 0.5491504 |
| 73006 | IFI44L | 79085586 | 79085586 | 0.6726998 | 0.7436687 | 0.0000910 | 0.9045692 | 0.4689935 | 0.7267674 | 0.0000000 | 0.6453144 |
| 219198 | IFITM1 | 313354 | 313354 | 0.2627358 | 0.3098730 | 0.0011124 | 0.8478823 | 0.4575495 | 0.4955707 | 0.0010769 | 0.9232780 |
| 157649 | PARP9 | 122281939 | 122281939 | 0.7183252 | 0.7916144 | 0.0015986 | 0.9074181 | 0.5414367 | 0.7888373 | 0.0000000 | 0.6863731 |
| 172157 | MX1 | 42798747 | 42798747 | 0.0572312 | 0.0650165 | 0.0024990 | 0.8802565 | 0.1408137 | 0.2300620 | 0.0000000 | 0.6120683 |
| 119415 | HELZ2 | 62199181 | 62199181 | 0.0651395 | 0.0373344 | 0.0055478 | 1.7447571 | 0.2184451 | 0.1198966 | 0.0000007 | 1.8219458 |
| 22822 | BRDT | 92417998 | 92417998 | 0.4365022 | 0.3211686 | 0.0259938 | 1.3591063 | 0.3998090 | 0.3770251 | 0.8765567 | 1.0604310 |
| 18023 | IFI44L | 79085765 | 79085765 | 0.4548280 | 0.4984651 | 0.0311206 | 0.9124571 | 0.2866716 | 0.4906685 | 0.0000000 | 0.5842471 |
| 427478 | FAM132A | 1178246 | 1178246 | 0.7422693 | 0.8213389 | 0.0357950 | 0.9037308 | 0.7160009 | 0.7586990 | 0.8705869 | 0.9437219 |
| 59750 | BRDT | 92414782 | 92414782 | 0.7324310 | 0.7659456 | 0.0385228 | 0.9562442 | 0.7921089 | 0.7686955 | 0.0684014 | 1.0304587 |
7.2 RA.PBL versus SSc.CD4+
| Gene | Cgsite | POS | McaM.SSc | McoM.SSc | Pvalue.SSc | FoldChange.SSc | McaM.RA | McoM.RA | Pvalue.RA | FoldChange.RA | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 194672 | EIF2AK2 | 37383568 | 37383568 | 0.1233814 | 0.1826725 | 0.0000315 | 0.6754238 | 0.1421435 | 0.1704233 | 0.0000000 | 0.8340613 |
| 204641 | PARP9 | 122281975 | 122281975 | 0.4276390 | 0.5290290 | 0.0000693 | 0.8083470 | 0.4976405 | 0.5300614 | 0.0000000 | 0.9388356 |
| 149108 | IFI44L | 79085586 | 79085586 | 0.6726998 | 0.7436687 | 0.0000910 | 0.9045692 | 0.4603852 | 0.5133334 | 0.0000000 | 0.8968542 |
| 353930 | IFITM1 | 313354 | 313354 | 0.2627358 | 0.3098730 | 0.0011124 | 0.8478823 | 0.6154195 | 0.5694498 | 0.0000000 | 1.0807266 |
| 210065 | PARP9 | 122281939 | 122281939 | 0.7183252 | 0.7916144 | 0.0015986 | 0.9074181 | 0.7600392 | 0.7673751 | 0.3881497 | 0.9904403 |
| 477689 | MX1 | 42798747 | 42798747 | 0.0572312 | 0.0650165 | 0.0024990 | 0.8802565 | 0.1401662 | 0.1484040 | 0.0088041 | 0.9444910 |
| 471312 | HELZ2 | 62199181 | 62199181 | 0.0651395 | 0.0373344 | 0.0055478 | 1.7447571 | 0.0710844 | 0.0676239 | 0.0002579 | 1.0511721 |
| 145961 | BRDT | 92417998 | 92417998 | 0.4365022 | 0.3211686 | 0.0259938 | 1.3591063 | 0.2402171 | 0.2392868 | 0.0195615 | 1.0038875 |
| 145476 | IFI44L | 79085765 | 79085765 | 0.4548280 | 0.4984651 | 0.0311206 | 0.9124571 | 0.1997635 | 0.2411714 | 0.0000000 | 0.8283051 |
| 173957 | FAM132A | 1178246 | 1178246 | 0.7422693 | 0.8213389 | 0.0357950 | 0.9037308 | 0.7583208 | 0.7458641 | 0.0000032 | 1.0167011 |
| 148183 | BRDT | 92414782 | 92414782 | 0.7324310 | 0.7659456 | 0.0385228 | 0.9562442 | 0.8080209 | 0.7812533 | 0.0000000 | 1.0342624 |
7.3 RA.PBL versus SSc.CD8+
| Gene | Cgsite | POS | McaM.SSc | McoM.SSc | Pvalue.SSc | FoldChange.SSc | McaM.RA | McoM.RA | Pvalue.RA | FoldChange.RA | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 204641 | PARP9 | 122281975 | 122281975 | 0.4531487 | 0.5968228 | 0.0000000 | 0.7592683 | 0.4976405 | 0.5300614 | 0.0000000 | 0.9388356 |
| 210065 | PARP9 | 122281939 | 122281939 | 0.7320359 | 0.8323341 | 0.0000001 | 0.8794977 | 0.7600392 | 0.7673751 | 0.3881497 | 0.9904403 |
| 194672 | EIF2AK2 | 37383568 | 37383568 | 0.1373269 | 0.1882193 | 0.0000971 | 0.7296114 | 0.1421435 | 0.1704233 | 0.0000000 | 0.8340613 |
| 471312 | HELZ2 | 62199181 | 62199181 | 0.0451481 | 0.0214664 | 0.0002035 | 2.1031944 | 0.0710844 | 0.0676239 | 0.0002579 | 1.0511721 |
| 451067 | TTC39C | 21572657 | 21572657 | 0.1848003 | 0.1419552 | 0.0003293 | 1.3018220 | 0.7481729 | 0.6888222 | 0.0000000 | 1.0861626 |
| 145476 | IFI44L | 79085765 | 79085765 | 0.5151405 | 0.6067145 | 0.0011990 | 0.8490656 | 0.1997635 | 0.2411714 | 0.0000000 | 0.8283051 |
| 449136 | TTC39C | 21572635 | 21572635 | 0.3820672 | 0.3329965 | 0.0054331 | 1.1473609 | 0.8068542 | 0.7577563 | 0.0000000 | 1.0647938 |
| 474109 | HELZ2 | 62199034 | 62199034 | 0.1427749 | 0.0981128 | 0.0069887 | 1.4552111 | 0.1275270 | 0.1322510 | 0.2553072 | 0.9642799 |
| 472712 | HELZ2 | 62199156 | 62199156 | 0.0221550 | 0.0106671 | 0.0071269 | 2.0769436 | 0.0818283 | 0.0769713 | 0.0000068 | 1.0631016 |
| 472275 | HELZ2 | 62199190 | 62199190 | 0.0334972 | 0.0185647 | 0.0096154 | 1.8043459 | 0.1084547 | 0.1054170 | 0.0120716 | 1.0288165 |
| 450014 | TTC39C | 21572623 | 21572623 | 0.3587072 | 0.3148537 | 0.0105301 | 1.1392822 | 0.7816516 | 0.7387071 | 0.0000000 | 1.0581347 |
| 167071 | IFI44L | 79085713 | 79085713 | 0.6866851 | 0.7410939 | 0.0116753 | 0.9265831 | 0.2537521 | 0.3171817 | 0.0000000 | 0.8000212 |
| 47063 | RNF39 | 30039476 | 30039476 | 0.3051805 | 0.3870814 | 0.0160688 | 0.7884144 | 0.1848225 | 0.1967838 | 0.0000164 | 0.9392162 |
| 149108 | IFI44L | 79085586 | 79085586 | 0.7097750 | 0.7625005 | 0.0178789 | 0.9308519 | 0.4603852 | 0.5133334 | 0.0000000 | 0.8968541 |
| 46471 | RNF39 | 30039403 | 30039403 | 0.4364698 | 0.5066883 | 0.0214113 | 0.8614167 | 0.2738635 | 0.3056240 | 0.0000005 | 0.8960799 |
| 275637 | RNF39 | 30039374 | 30039374 | 0.2453951 | 0.3210745 | 0.0227590 | 0.7642931 | 0.1846558 | 0.2014602 | 0.0000081 | 0.9165874 |
| 48849 | RNF39 | 30039466 | 30039466 | 0.2398981 | 0.3018692 | 0.0269289 | 0.7947089 | 0.2981943 | 0.3105540 | 0.0000390 | 0.9602013 |
| 47649 | RNF39 | 30039435 | 30039435 | 0.4457716 | 0.5147477 | 0.0368050 | 0.8660003 | 0.2603282 | 0.2891516 | 0.0000008 | 0.9003174 |
| 47925 | RNF39 | 30039432 | 30039432 | 0.4890092 | 0.5487349 | 0.0445974 | 0.8911575 | 0.2723385 | 0.3041660 | 0.0000004 | 0.8953613 |